[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/11541723/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/10689405/transformed.cor.cli.txt"

nPatients in clinical file=349, in cluster file=278, common to both=276
[1] 147 276
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            86            190 
  NRAS MUTATED NRAS WILD-TYPE 
            86            190 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            47            229 
  TP53 MUTATED TP53 WILD-TYPE 
            47            229 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              41              235 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              41              235 
[1] "RPS27 MUTATION ANALYSIS"
[1] 3
  RPS27 MUTATED RPS27 WILD-TYPE 
             23             253 
  RPS27 MUTATED RPS27 WILD-TYPE 
             23             253 
[1] "MRPS31 MUTATION ANALYSIS"
[1] 3
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              257 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              257 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           38           238 
  NF1 MUTATED NF1 WILD-TYPE 
           38           238 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            256 
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            256 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             35             241 
  ARID2 MUTATED ARID2 WILD-TYPE 
             35             241 
[1] "C15ORF23 MUTATION ANALYSIS"
[1] 3
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                19                257 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                19                257 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            23            253 
  PTEN MUTATED PTEN WILD-TYPE 
            23            253 
[1] "NOTCH2NL MUTATION ANALYSIS"
[1] 3
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                261 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                261 
[1] "MAP2K1 MUTATION ANALYSIS"
[1] 3
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              12              264 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              12              264 
[1] "PPP6C MUTATION ANALYSIS"
[1] 3
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             256 
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             256 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            15            261 
  IDH1 MUTATED IDH1 WILD-TYPE 
            15            261 
[1] "PDE1A MUTATION ANALYSIS"
[1] 3
  PDE1A MUTATED PDE1A WILD-TYPE 
             39             237 
  PDE1A MUTATED PDE1A WILD-TYPE 
             39             237 
[1] "HMGCR MUTATION ANALYSIS"
[1] 3
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             265 
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             265 
[1] "PHGDH MUTATION ANALYSIS"
[1] 3
  PHGDH MUTATED PHGDH WILD-TYPE 
             11             265 
  PHGDH MUTATED PHGDH WILD-TYPE 
             11             265 
[1] "SLC38A4 MUTATION ANALYSIS"
[1] 3
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               34               242 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               34               242 
[1] "CDK4 MUTATION ANALYSIS"
[1] 3
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            269 
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            269 
[1] "FAM58A MUTATION ANALYSIS"
[1] 3
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              271 
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              271 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            268 
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            268 
[1] "RQCD1 MUTATION ANALYSIS"
[1] 3
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              9             267 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              9             267 
[1] "HSD11B1 MUTATION ANALYSIS"
[1] 3
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               262 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               262 
[1] "DMC1 MUTATION ANALYSIS"
[1] 3
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            264 
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            264 
[1] "NRK MUTATION ANALYSIS"
[1] 3
  NRK MUTATED NRK WILD-TYPE 
           43           233 
  NRK MUTATED NRK WILD-TYPE 
           43           233 
[1] "TAF1A MUTATION ANALYSIS"
[1] 3
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             263 
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             263 
[1] "OXA1L MUTATION ANALYSIS"
[1] 3
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             268 
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             268 
[1] "COL3A1 MUTATION ANALYSIS"
[1] 3
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              56              220 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              56              220 
[1] "TCHHL1 MUTATION ANALYSIS"
[1] 3
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              39              237 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              39              237 
[1] "IL5RA MUTATION ANALYSIS"
[1] 3
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             259 
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             259 
[1] "NBPF7 MUTATION ANALYSIS"
[1] 3
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             263 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             263 
[1] "KEL MUTATION ANALYSIS"
[1] 3
  KEL MUTATED KEL WILD-TYPE 
           36           240 
  KEL MUTATED KEL WILD-TYPE 
           36           240 
[1] "C7ORF58 MUTATION ANALYSIS"
[1] 3
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               34               242 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               34               242 
[1] "NBPF1 MUTATION ANALYSIS"
[1] 3
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             39             237 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             39             237 
[1] "TMEM216 MUTATION ANALYSIS"
[1] 3
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               268 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               268 
[1] "DOM3Z MUTATION ANALYSIS"
[1] 3
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              7             269 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              7             269 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              48              228 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              48              228 
[1] "ZFX MUTATION ANALYSIS"
[1] 3
  ZFX MUTATED ZFX WILD-TYPE 
           13           263 
  ZFX MUTATED ZFX WILD-TYPE 
           13           263 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           139            137 
  BRAF MUTATED BRAF WILD-TYPE 
           139            137 
[1] "SAG MUTATION ANALYSIS"
[1] 3
  SAG MUTATED SAG WILD-TYPE 
           11           265 
  SAG MUTATED SAG WILD-TYPE 
           11           265 
[1] "OR51S1 MUTATION ANALYSIS"
[1] 3
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              30              246 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              30              246 
[1] "USP17L2 MUTATION ANALYSIS"
[1] 3
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               22               254 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               22               254 
[1] "LRPPRC MUTATION ANALYSIS"
[1] 3
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              15              261 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              15              261 
[1] "BTK MUTATION ANALYSIS"
[1] 3
  BTK MUTATED BTK WILD-TYPE 
           16           260 
  BTK MUTATED BTK WILD-TYPE 
           16           260 
[1] "DSG3 MUTATION ANALYSIS"
[1] 3
  DSG3 MUTATED DSG3 WILD-TYPE 
            47            229 
  DSG3 MUTATED DSG3 WILD-TYPE 
            47            229 
[1] "C1QTNF9 MUTATION ANALYSIS"
[1] 3
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               260 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               260 
[1] "BLM MUTATION ANALYSIS"
[1] 3
  BLM MUTATED BLM WILD-TYPE 
           15           261 
  BLM MUTATED BLM WILD-TYPE 
           15           261 
[1] "ACSM2B MUTATION ANALYSIS"
[1] 3
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              44              232 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              44              232 
[1] "PARM1 MUTATION ANALYSIS"
[1] 3
  PARM1 MUTATED PARM1 WILD-TYPE 
             19             257 
  PARM1 MUTATED PARM1 WILD-TYPE 
             19             257 
[1] "TP63 MUTATION ANALYSIS"
[1] 3
  TP63 MUTATED TP63 WILD-TYPE 
            48            228 
  TP63 MUTATED TP63 WILD-TYPE 
            48            228 
[1] "NGF MUTATION ANALYSIS"
[1] 3
  NGF MUTATED NGF WILD-TYPE 
            9           267 
  NGF MUTATED NGF WILD-TYPE 
            9           267 
[1] "ANO4 MUTATION ANALYSIS"
[1] 3
  ANO4 MUTATED ANO4 WILD-TYPE 
            44            232 
  ANO4 MUTATED ANO4 WILD-TYPE 
            44            232 
[1] "PCDH18 MUTATION ANALYSIS"
[1] 3
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              50              226 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              50              226 
[1] "NMS MUTATION ANALYSIS"
[1] 3
  NMS MUTATED NMS WILD-TYPE 
           13           263 
  NMS MUTATED NMS WILD-TYPE 
           13           263 
[1] "C12ORF43 MUTATION ANALYSIS"
[1] 3
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                271 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                271 
[1] "XIRP2 MUTATION ANALYSIS"
[1] 3
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             93             183 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             93             183 
[1] "USH2A MUTATION ANALYSIS"
[1] 3
  USH2A MUTATED USH2A WILD-TYPE 
             91             185 
  USH2A MUTATED USH2A WILD-TYPE 
             91             185 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
             19             257 
  DDX3X MUTATED DDX3X WILD-TYPE 
             19             257 
[1] "PTPN22 MUTATION ANALYSIS"
[1] 3
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              24              252 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              24              252 
[1] "C3ORF71 MUTATION ANALYSIS"
[1] 3
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               272 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               272 
[1] "CEACAM6 MUTATION ANALYSIS"
[1] 3
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               261 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               261 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
            17            259 
  MUC7 MUTATED MUC7 WILD-TYPE 
            17            259 
[1] "SELP MUTATION ANALYSIS"
[1] 3
  SELP MUTATED SELP WILD-TYPE 
            34            242 
  SELP MUTATED SELP WILD-TYPE 
            34            242 
[1] "LIPH MUTATION ANALYSIS"
[1] 3
  LIPH MUTATED LIPH WILD-TYPE 
            15            261 
  LIPH MUTATED LIPH WILD-TYPE 
            15            261 
[1] "MMP1 MUTATION ANALYSIS"
[1] 3
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            262 
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            262 
[1] "KLF11 MUTATION ANALYSIS"
[1] 3
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             267 
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             267 
[1] "USP9X MUTATION ANALYSIS"
[1] 3
  USP9X MUTATED USP9X WILD-TYPE 
             15             261 
  USP9X MUTATED USP9X WILD-TYPE 
             15             261 
[1] "PTK7 MUTATION ANALYSIS"
[1] 3
  PTK7 MUTATED PTK7 WILD-TYPE 
            17            259 
  PTK7 MUTATED PTK7 WILD-TYPE 
            17            259 
[1] "SLC14A1 MUTATION ANALYSIS"
[1] 3
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               18               258 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               18               258 
[1] "PROX2 MUTATION ANALYSIS"
[1] 3
  PROX2 MUTATED PROX2 WILD-TYPE 
             13             263 
  PROX2 MUTATED PROX2 WILD-TYPE 
             13             263 
[1] "DNMBP MUTATION ANALYSIS"
[1] 3
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             257 
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             257 
[1] "MPP7 MUTATION ANALYSIS"
[1] 3
  MPP7 MUTATED MPP7 WILD-TYPE 
            30            246 
  MPP7 MUTATED MPP7 WILD-TYPE 
            30            246 
[1] "IFNGR2 MUTATION ANALYSIS"
[1] 3
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              272 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              272 
[1] "ASNSD1 MUTATION ANALYSIS"
[1] 3
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               7              269 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               7              269 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            9           267 
  RB1 MUTATED RB1 WILD-TYPE 
            9           267 
[1] "CCK MUTATION ANALYSIS"
[1] 3
  CCK MUTATED CCK WILD-TYPE 
            6           270 
  CCK MUTATED CCK WILD-TYPE 
            6           270 
[1] "ZNF780B MUTATION ANALYSIS"
[1] 3
  ZNF780B MUTATED ZNF780B WILD-TYPE 
               10               266 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
               10               266 
[1] "ATP5F1 MUTATION ANALYSIS"
[1] 3
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              269 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              269 
[1] "LOC728819 MUTATION ANALYSIS"
[1] 3
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  8                 268 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  8                 268 
[1] "LACRT MUTATION ANALYSIS"
[1] 3
  LACRT MUTATED LACRT WILD-TYPE 
              9             267 
  LACRT MUTATED LACRT WILD-TYPE 
              9             267 
[1] "RPGRIP1 MUTATION ANALYSIS"
[1] 3
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               25               251 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               25               251 
[1] "THEMIS MUTATION ANALYSIS"
[1] 3
  THEMIS MUTATED THEMIS WILD-TYPE 
              33              243 
  THEMIS MUTATED THEMIS WILD-TYPE 
              33              243 
[1] "PTPRT MUTATION ANALYSIS"
[1] 3
  PTPRT MUTATED PTPRT WILD-TYPE 
             80             196 
  PTPRT MUTATED PTPRT WILD-TYPE 
             80             196 
[1] "SELPLG MUTATION ANALYSIS"
[1] 3
  SELPLG MUTATED SELPLG WILD-TYPE 
              10              266 
  SELPLG MUTATED SELPLG WILD-TYPE 
              10              266 
[1] "CSN3 MUTATION ANALYSIS"
[1] 3
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            272 
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            272 
[1] "SLC7A11 MUTATION ANALYSIS"
[1] 3
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               11               265 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               11               265 
[1] "SYNE1 MUTATION ANALYSIS"
[1] 3
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             73             203 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             73             203 
[1] "NFASC MUTATION ANALYSIS"
[1] 3
  NFASC MUTATED NFASC WILD-TYPE 
             22             254 
  NFASC MUTATED NFASC WILD-TYPE 
             22             254 
[1] "CCDC11 MUTATION ANALYSIS"
[1] 3
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              259 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              259 
[1] "IL31RA MUTATION ANALYSIS"
[1] 3
  IL31RA MUTATED IL31RA WILD-TYPE 
              17              259 
  IL31RA MUTATED IL31RA WILD-TYPE 
              17              259 
[1] "MLL MUTATION ANALYSIS"
[1] 3
  MLL MUTATED MLL WILD-TYPE 
           38           238 
  MLL MUTATED MLL WILD-TYPE 
           38           238 
[1] "DIRC2 MUTATION ANALYSIS"
[1] 3
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             272 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             272 
[1] "ADAM22 MUTATION ANALYSIS"
[1] 3
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              257 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              257 
[1] "PLCXD2 MUTATION ANALYSIS"
[1] 3
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               9              267 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               9              267 
[1] "EDN1 MUTATION ANALYSIS"
[1] 3
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            267 
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            267 
[1] "HTR7 MUTATION ANALYSIS"
[1] 3
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            267 
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            267 
[1] "TLR9 MUTATION ANALYSIS"
[1] 3
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            258 
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            258 
[1] "MYH1 MUTATION ANALYSIS"
[1] 3
  MYH1 MUTATED MYH1 WILD-TYPE 
            67            209 
  MYH1 MUTATED MYH1 WILD-TYPE 
            67            209 
[1] "EPHA3 MUTATION ANALYSIS"
[1] 3
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             30             246 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             30             246 
[1] "ARL16 MUTATION ANALYSIS"
[1] 3
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             269 
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             269 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             265 
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             265 
[1] "MAN1A1 MUTATION ANALYSIS"
[1] 3
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              14              262 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              14              262 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              28              248 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              28              248 
[1] "NBEAL1 MUTATION ANALYSIS"
[1] 3
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              30              246 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              30              246 
[1] "WDR65 MUTATION ANALYSIS"
[1] 3
  WDR65 MUTATED WDR65 WILD-TYPE 
             21             255 
  WDR65 MUTATED WDR65 WILD-TYPE 
             21             255 
[1] "C6ORF165 MUTATION ANALYSIS"
[1] 3
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                19                257 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                19                257 
[1] "RNF133 MUTATION ANALYSIS"
[1] 3
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              268 
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              268 
[1] "GTPBP4 MUTATION ANALYSIS"
[1] 3
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              268 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              268 
[1] "ACSBG1 MUTATION ANALYSIS"
[1] 3
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              12              264 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              12              264 
[1] "TPTE MUTATION ANALYSIS"
[1] 3
  TPTE MUTATED TPTE WILD-TYPE 
            60            216 
  TPTE MUTATED TPTE WILD-TYPE 
            60            216 
[1] "CLCC1 MUTATION ANALYSIS"
[1] 3
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             263 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             263 
[1] "PPAP2B MUTATION ANALYSIS"
[1] 3
  PPAP2B MUTATED PPAP2B WILD-TYPE 
              10              266 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
              10              266 
[1] "CD300E MUTATION ANALYSIS"
[1] 3
  CD300E MUTATED CD300E WILD-TYPE 
              10              266 
  CD300E MUTATED CD300E WILD-TYPE 
              10              266 
[1] "ALDH5A1 MUTATION ANALYSIS"
[1] 3
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               266 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               266 
[1] "SPRYD3 MUTATION ANALYSIS"
[1] 3
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               8              268 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               8              268 
[1] "MAP3K5 MUTATION ANALYSIS"
[1] 3
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              19              257 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              19              257 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             267 
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             267 
[1] "SNCAIP MUTATION ANALYSIS"
[1] 3
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              48              228 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              48              228 
[1] "HLA-DRA MUTATION ANALYSIS"
[1] 3
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               12               264 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               12               264 
[1] "ACTC1 MUTATION ANALYSIS"
[1] 3
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             261 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             261 
[1] "ELOVL3 MUTATION ANALYSIS"
[1] 3
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              271 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              271 
[1] "THSD7B MUTATION ANALYSIS"
[1] 3
  THSD7B MUTATED THSD7B WILD-TYPE 
              88              188 
  THSD7B MUTATED THSD7B WILD-TYPE 
              88              188 
[1] "SLC27A5 MUTATION ANALYSIS"
[1] 3
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               268 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               268 
[1] "PDE4DIP MUTATION ANALYSIS"
[1] 3
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               44               232 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               44               232 
[1] "KANK3 MUTATION ANALYSIS"
[1] 3
  KANK3 MUTATED KANK3 WILD-TYPE 
              8             268 
  KANK3 MUTATED KANK3 WILD-TYPE 
              8             268 
[1] "RUNX1T1 MUTATION ANALYSIS"
[1] 3
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               34               242 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               34               242 
[1] "WDR12 MUTATION ANALYSIS"
[1] 3
  WDR12 MUTATED WDR12 WILD-TYPE 
             11             265 
  WDR12 MUTATED WDR12 WILD-TYPE 
             11             265 
[1] "POTEG MUTATION ANALYSIS"
[1] 3
  POTEG MUTATED POTEG WILD-TYPE 
             31             245 
  POTEG MUTATED POTEG WILD-TYPE 
             31             245 
[1] "ITPR2 MUTATION ANALYSIS"
[1] 3
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             16             260 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             16             260 
[1] "CRNKL1 MUTATION ANALYSIS"
[1] 3
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              13              263 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              13              263 
[1] "DSP MUTATION ANALYSIS"
[1] 3
  DSP MUTATED DSP WILD-TYPE 
           59           217 
  DSP MUTATED DSP WILD-TYPE 
           59           217 
[1] "SF3B1 MUTATION ANALYSIS"
[1] 3
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             263 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             263 
[1] "CAGE1 MUTATION ANALYSIS"
[1] 3
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             265 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             265 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             265 
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             265 
[1] "CYP3A7 MUTATION ANALYSIS"
[1] 3
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              25              251 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              25              251 
[1] "VGLL1 MUTATION ANALYSIS"
[1] 3
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             270 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             270 
[1] "GML MUTATION ANALYSIS"
[1] 3
  GML MUTATED GML WILD-TYPE 
           10           266 
  GML MUTATED GML WILD-TYPE 
           10           266 
[1] "GZMA MUTATION ANALYSIS"
[1] 3
  GZMA MUTATED GZMA WILD-TYPE 
            11            265 
  GZMA MUTATED GZMA WILD-TYPE 
            11            265 
[1] "NPTX1 MUTATION ANALYSIS"
[1] 3
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             268 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             268 
[1] "DACT1 MUTATION ANALYSIS"
[1] 3
  DACT1 MUTATED DACT1 WILD-TYPE 
             13             263 
  DACT1 MUTATED DACT1 WILD-TYPE 
             13             263 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
             13             263 
  STK19 MUTATED STK19 WILD-TYPE 
             13             263 
[1] "STK31 MUTATION ANALYSIS"
[1] 3
  STK31 MUTATED STK31 WILD-TYPE 
             35             241 
  STK31 MUTATED STK31 WILD-TYPE 
             35             241 
[1] "ROS1 MUTATION ANALYSIS"
[1] 3
  ROS1 MUTATED ROS1 WILD-TYPE 
            56            220 
  ROS1 MUTATED ROS1 WILD-TYPE 
            56            220 
[1] "KCNB2 MUTATION ANALYSIS"
[1] 3
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             58             218 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             58             218 
[1] "ART3 MUTATION ANALYSIS"
[1] 3
  ART3 MUTATED ART3 WILD-TYPE 
            12            264 
  ART3 MUTATED ART3 WILD-TYPE 
            12            264 
[1] "CLDN4 MUTATION ANALYSIS"
[1] 3
  CLDN4 MUTATED CLDN4 WILD-TYPE 
             11             265 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
             11             265 
[1] "RAG2 MUTATION ANALYSIS"
[1] 3
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            258 
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            258 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDISEASE"                  
 [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 276 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         2639           NA 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
        1888           NA         1280           NA         5219         1709 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 
        2010         1812         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         1378         5318 
TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
        1695           NA         1714         4414         1002          688 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
        1941          818         4129         4195         5424          553 
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 
         678          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         2076 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        1643          526         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 
        4070           NA         2785           NA           NA           NA 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        2452         1455           NA         1940           NA         1966 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
          NA         1729           NA         1716         1136          440 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        1701           NA         5932           NA           NA         3130 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
        1120           NA         2620         1803         2051         9568 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        4898         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         3857           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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA         4825         6176           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
        7563           NA         4088         4942         2166         1620 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        3781         3733         1570          112         1658           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
         714           NA           NA           NA           NA         1949 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
          NA           NA         6138           NA         1562         3333 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
        4504           NA           NA           NA           NA           NA 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        2365           NA           NA           NA           NA           NA 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        8180           NA           NA           NA           NA         1340 
TCGA-ER-A19O TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
          NA           NA           NA         1133           NA           NA 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
        2433           NA           NA           NA          498          951 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
         975           NA         2443         1429         1010          206 
TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        2828           NA         5299          478           NA           NA 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
          NA           NA           NA         1225           NA           NA 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
          NA           NA           NA         3080           NA           NA 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
          NA         4526         1617           NA         1505           NA 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
          NA         2367           NA           NA           NA          378 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
          NA         1504         2369            6          697         1446 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
           5          587          301          220           62          357 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        4255           NA         2577           NA           NA           NA 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-RP-A695 
          NA         1204          203           10           21           NA 
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=140,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=144,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=218,	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=112,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=29,	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=13,	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 276 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 
22 30 59 54 57 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   52    59    54    57 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
22 30 59 54 57 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   52    59    54    57 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
139  48  33  36 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
139  48  33  36 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
139  48  33  36 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
139  48  33  36 
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=112, 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   35 49
  NRAS WILD-TYPE 91 91
  NRAS MUTATED NRAS WILD-TYPE 
            84            182 
  NRAS MUTATED NRAS WILD-TYPE 
            49             91 
$`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        29.23        93.21        32.61        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-EB-A5UL TCGA-EE-A17X TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       23.15        13.35        11.57         5.13         4.31         4.34 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        8.55         1.08         8.09         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GJ 
        8.09        49.22        36.30         9.67        17.98        19.43 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2MC 
       35.54        28.31        33.83         5.42        36.33        47.51 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MU 
        9.53         2.73       111.91        56.02        25.08         5.56 
TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 
       51.62        21.60        16.14        22.22        33.60        18.61 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE 
        5.72         3.52        42.84        17.72        11.80         1.51 
TCGA-ER-A2NH TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       11.74        18.41        15.72        64.47        23.80        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
        7.30         3.39        19.53        52.08         8.65        40.64 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
       27.39         0.82         5.23        28.73        10.78         6.41 
TCGA-FS-A4FD TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A267 TCGA-GN-A268 TCGA-RP-A694 
        2.27         9.90        11.61        16.24        15.42         0.69 

$`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 
       86.76        11.41        44.19         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        59.57       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        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       25.78        52.01        13.68        17.72        23.11        21.93 
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        19.00        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 
       60.23        15.85         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        62.79        36.85        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       12.03        32.15        11.31        36.33        51.12        34.29 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR 
       60.00        47.21        30.08        16.01        55.69         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       125.65 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       26.99        21.60        60.49        53.16        52.67       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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
        3.22        22.92        21.60         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       21.73        31.40        12.95        38.40        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78        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-A19T 
       13.45        28.60        34.68         9.57        36.07         6.58 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44         1.87        13.08        12.62         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1YY 
       22.49         1.71         5.62        85.74         3.45        11.01 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       15.52         7.33        20.38         8.22        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        12.89        47.38         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 
        8.68        53.85         7.36        14.20         5.98         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
        0.99         0.13         0.16        17.33         7.23         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       44.28        31.33        84.72        10.13        12.16        14.70 
TCGA-QB-A6FS TCGA-RP-A693 
        5.79         0.33 

  NRAS MUTATED NRAS WILD-TYPE 
          0.20           0.13 
  NRAS MUTATED NRAS WILD-TYPE 
        111.91         125.65 
  NRAS MUTATED NRAS WILD-TYPE 
        15.570         18.705 
[1] "0.2 - 111.9 (15.6)" "0.1 - 125.7 (18.7)"
[1] "hr=" "1.4"
D1V2, survival
                sevent
clus2             0  1
  NRAS MUTATED   35 49
  NRAS WILD-TYPE 94 92
  NRAS MUTATED NRAS WILD-TYPE 
            84            186 
  NRAS MUTATED NRAS WILD-TYPE 
            49             92 
$`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        45.30       174.84        63.81       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 
       68.25        17.29        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        36.82        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-A2MF TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MU 
       47.28       268.73       203.05       167.90        47.54        53.26 
TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 
       51.62        64.08        34.32        53.19       148.08        35.44 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE 
        9.17        12.59        44.05       148.18        43.82        20.15 
TCGA-ER-A2NH TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       32.05        92.98        15.72       216.92       202.65        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       27.72        48.85        40.27        74.73       133.55        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
       49.48        27.09        27.02        28.73        12.43        49.45 
TCGA-FS-A4FD TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A267 TCGA-GN-A268 TCGA-RP-A694 
       77.88         9.90        11.74        64.44        62.79         0.69 

$`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 
       86.76        11.87        62.07       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        59.57       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        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       26.89       135.75       178.32        18.18       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        22.29         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        54.02        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       133.81        91.56 
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 
       63.78        64.64        56.84        18.61        56.42       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82        86.14        59.28        67.43       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       48.72        54.74       126.81        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       158.63       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      134.40       162.48        71.21       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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       36.95       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       13.94        50.76        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2ND 
      162.08        50.89        37.25         8.88        79.99        23.34 
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-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        6.77       174.21        48.59       228.59        28.08         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A4F0 
       23.93       101.26        11.41       148.80        26.56        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       66.67       174.84        26.73         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16        19.30         7.23         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       84.72        10.13        32.48        39.58         6.67         0.33 

  NRAS MUTATED NRAS WILD-TYPE 
          0.69           0.16 
  NRAS MUTATED NRAS WILD-TYPE 
        314.56         357.37 
  NRAS MUTATED NRAS WILD-TYPE 
        48.870         54.265 
[1] "0.7 - 314.6 (48.9)" "0.2 - 357.4 (54.3)"
[1] "hr=" "1.3"
D1V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  NRAS MUTATED                   18             1
  NRAS WILD-TYPE                 21             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NRAS MUTATED                                          19                  48
  NRAS WILD-TYPE                                        41                 123
D1V4, multiclass
                                           clus
vv                                          NRAS MUTATED NRAS WILD-TYPE
  DISTANT METASTASIS                                  18             21
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           19             41
  REGIONAL LYMPH NODE                                 48            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       6        5       11        5
  NRAS WILD-TYPE           7       3      18        5       13       11
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NRAS MUTATED           5         5         2         4          4          8
  NRAS WILD-TYPE         5         9         7        28          9         15
                vv
clus             STAGE IIIC STAGE IV
  NRAS MUTATED           17        4
  NRAS WILD-TYPE         29       12
D1V5, multiclass
             clus
vv            NRAS MUTATED NRAS WILD-TYPE
  I OR II NOS            3              7
  STAGE 0                3              3
  STAGE I                6             18
  STAGE IA               5              5
  STAGE IB              11             13
  STAGE II               5             11
  STAGE IIA              5              5
  STAGE IIB              5              9
  STAGE IIC              2              7
  STAGE III              4             28
  STAGE IIIA             4              9
  STAGE IIIB             8             15
  STAGE IIIC            17             29
  STAGE IV               4             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
  NRAS MUTATED      13 23 15 17
  NRAS WILD-TYPE    39 36 39 40
D1V6, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  T0+T1           13             39
  T2              23             36
  T3              15             39
  T4              17             40
[1] 4 2
[1] TRUE
[1] "dimension of 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   47  9  9 15
  NRAS WILD-TYPE 92 39 24 21
D1V7, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0           47             92
  N1            9             39
  N2            9             24
  N3           15             21
[1] 4 2
[1] 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    77   1   0   1   2
  NRAS WILD-TYPE 167   3   3   1   6
D1V8, multiclass
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  M0            77            167
  M1             1              3
  M1A            0              3
  M1B            1              1
  M1C            2              6
[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 68 46
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     35   22
  NRAS WILD-TYPE   68   46
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            35             68
  YES           22             46
[1] 2 2
[1] FALSE
D1V10, binary
                cls
clus               0   1
  NRAS MUTATED    11  75
  NRAS WILD-TYPE  25 164
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     11   75
  NRAS WILD-TYPE   25  164
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            11             25
  YES           75            164
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, binary
                cls
clus               0   1
  NRAS MUTATED    31  55
  NRAS WILD-TYPE  75 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     31   55
  NRAS WILD-TYPE   75  115
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           31             75
  MALE             55            115
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       2                         0    84
  NRAS WILD-TYPE     1                         1   188
D1V13, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                2              1
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               84            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"
D1V14, binary
                cls
clus               0   1
  NRAS MUTATED     1  84
  NRAS WILD-TYPE   2 185
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1   84
  NRAS WILD-TYPE    2  185
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           84            185
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    26  20
  TP53 WILD-TYPE 100 120
  TP53 MUTATED TP53 WILD-TYPE 
            46            220 
  TP53 MUTATED TP53 WILD-TYPE 
            20            120 
$`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        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I5 
       13.68        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        62.79         1.08        39.62         2.43         8.09 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2MG 
       36.30        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-GF-A6C9 TCGA-GN-A266 
        0.99         0.85        11.61        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        86.76        11.41        44.19         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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       32.61        17.72        23.11         4.01        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15         8.55        36.85         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        8.84         9.99        32.15        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        17.98        60.00        47.21        30.08 
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        55.69         1.15 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46         2.73         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       63.42       125.65       111.91        25.08        26.99        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH 
       53.16        52.67       122.73        51.62        13.81        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
        3.22        22.92        22.22         0.95        18.41        21.73 
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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       13.08        12.62        11.74         9.04        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        23.80        14.24         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-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        17.33         9.90         7.23 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  TP53 MUTATED TP53 WILD-TYPE 
          0.85           0.13 
  TP53 MUTATED TP53 WILD-TYPE 
        124.31         125.65 
  TP53 MUTATED TP53 WILD-TYPE 
        21.600         16.125 
[1] "0.8 - 124.3 (21.6)" "0.1 - 125.7 (16.1)"
[1] "hr=" "1.3"
D2V2, survival
                sevent
clus2              0   1
  TP53 MUTATED    26  20
  TP53 WILD-TYPE 103 121
  TP53 MUTATED TP53 WILD-TYPE 
            46            224 
  TP53 MUTATED TP53 WILD-TYPE 
            20            121 
$`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        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I5 
      178.32        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        63.78         2.60        56.84        25.87        17.92 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2MG 
       36.82        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-GF-A6C9 TCGA-GN-A266 
       22.92         2.04        11.74        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        86.76        11.87        62.07       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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       63.81        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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 
       64.64        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 
      195.02        46.82       102.90        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       268.73        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      203.05        47.54       248.65       134.40       162.48        71.21 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        51.62        13.81       138.81       172.18       127.20 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       53.19       201.80        51.35       109.58        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-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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       32.05       247.04        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91         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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        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-GN-A262 TCGA-GN-A264 
        0.16        19.30         9.90         7.23       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  TP53 MUTATED TP53 WILD-TYPE 
          2.04           0.16 
  TP53 MUTATED TP53 WILD-TYPE 
        178.32         357.37 
  TP53 MUTATED TP53 WILD-TYPE 
        44.055         53.720 
[1] "2.0 - 178.3 (44.1)" "0.2 - 357.4 (53.7)"
[1] "hr=" "1.1"
D2V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TP53 MUTATED                    4             2
  TP53 WILD-TYPE                 35             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TP53 MUTATED                                          11                  30
  TP53 WILD-TYPE                                        49                 141
D2V4, multiclass
                                           clus
vv                                          TP53 MUTATED TP53 WILD-TYPE
  DISTANT METASTASIS                                   4             35
  PRIMARY TUMOR                                        2              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           11             49
  REGIONAL LYMPH NODE                                 30            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
  TP53 MUTATED             0       1       6        3        4        2
  TP53 WILD-TYPE          10       5      18        7       20       14
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TP53 MUTATED           1         2         0         7          5          6
  TP53 WILD-TYPE         9        12         9        25          8         17
                vv
clus             STAGE IIIC STAGE IV
  TP53 MUTATED            8        1
  TP53 WILD-TYPE         38       15
D2V5, multiclass
             clus
vv            TP53 MUTATED TP53 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                6             18
  STAGE IA               3              7
  STAGE IB               4             20
  STAGE II               2             14
  STAGE IIA              1              9
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              7             25
  STAGE IIIA             5              8
  STAGE IIIB             6             17
  STAGE IIIC             8             38
  STAGE IV               1             15
[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    40 49 45 47
D2V6, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           12             40
  T2              10             49
  T3               9             45
  T4              10             47
[1] 4 2
[1] TRUE
[1] "dimension of 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  14   6   5
  TP53 WILD-TYPE 120  34  27  31
D2V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           19            120
  N1           14             34
  N2            6             27
  N3            5             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
  TP53 MUTATED    44   0   0   0   1
  TP53 WILD-TYPE 200   4   3   2   7
D2V8, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  M0            44            200
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            1              7
[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 84 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     19   11
  TP53 WILD-TYPE   84   57
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            19             84
  YES           11             57
[1] 2 2
[1] FALSE
D2V10, binary
                cls
clus               0   1
  TP53 MUTATED     7  40
  TP53 WILD-TYPE  29 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      7   40
  TP53 WILD-TYPE   29  199
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             7             29
  YES           40            199
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, binary
                cls
clus               0   1
  TP53 MUTATED    18  29
  TP53 WILD-TYPE  88 141
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     18   29
  TP53 WILD-TYPE   88  141
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           18             88
  MALE             29            141
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0    47
  TP53 WILD-TYPE     3                         1   225
D2V13, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               47            225
[1] 3 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  47
  TP53 WILD-TYPE   3 222
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   47
  TP53 WILD-TYPE    3  222
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           47            222
[1] 2 2
[1] FALSE

Clustering(3) Variable = CDKN2A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    22  17
  CDKN2A WILD-TYPE 104 123
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              39              227 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              17              123 
$`CDKN2A MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3CB TCGA-D3-A3MV 
      111.09        11.41        44.19         6.31        82.29        29.23 
TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EC 
       54.31        52.01        13.68        17.72         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        60.23        62.79 
TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2M5 
        2.43        36.33        34.29        28.31         5.42         8.84 
TCGA-EE-A2MD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD 
        9.53        30.15        15.95        21.60         0.95        27.35 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1ZQ TCGA-FS-A1ZW 
        3.52        13.45        34.68        64.47         8.65        27.39 
TCGA-GF-A4EO TCGA-GN-A26A TCGA-RP-A694 
        7.23        12.16         0.69 

$`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        86.76         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        59.57       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        93.21        54.74        31.30 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
       32.28        21.44        32.61        25.78        47.87        23.11 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
       21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        5.13         4.34        15.85         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        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       51.12        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        33.83        55.69         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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         3.68        13.81        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        22.22        18.41        21.73        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-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        4.21        28.60        42.84         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1YY 
        5.62        18.41        85.74        15.72         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-A1ZR TCGA-FS-A1ZS 
       12.92        12.89        47.38        52.08         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64         8.68         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        17.33         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        14.70         5.79         0.33 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.69             0.13 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          111.09           125.65 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           17.72            16.47 
[1] "0.7 - 111.1 (17.7)" "0.1 - 125.7 (16.5)"
[1] "hr=" "1.2"
D3V2, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    22  17
  CDKN2A WILD-TYPE 107 124
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              39              231 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              17              124 
$`CDKN2A MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3CB TCGA-D3-A3MV 
      112.04        11.87        62.07        12.10       166.52        45.30 
TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EC 
      145.12       135.75       178.32        18.18        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       133.81        63.78 
TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2M5 
       25.87        86.14        67.43        75.48        13.91        21.67 
TCGA-EE-A2MD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD 
       47.28        54.51        23.47        64.08       201.80        27.35 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1ZQ TCGA-FS-A1ZW 
       12.59       131.51       162.08       216.92       133.55        49.48 
TCGA-GF-A4EO TCGA-GN-A26A TCGA-RP-A694 
        7.23        32.48         0.69 

$`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        86.76       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        59.57       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       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
       32.94        22.62        63.81        26.89       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        22.29         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 
       68.25        54.02        17.29        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 
       91.56       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        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD 
       46.82       102.90        36.82        39.29        59.28       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF 
      129.27        28.83        19.76        61.51       103.27       268.73 
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       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       53.19        51.35       109.58       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-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       13.02        26.37       268.93       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      174.21        15.72        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-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-A6C8 TCGA-GF-A6C9 
       47.54         0.16        19.30         9.90         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       39.58         6.67         0.33 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.69             0.16 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          216.92           357.37 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           54.51            51.62 
[1] "0.7 - 216.9 (54.5)" "0.2 - 357.4 (51.6)"
[1] "hr=" "1.2"
D3V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CDKN2A MUTATED                    6             1
  CDKN2A WILD-TYPE                 33             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CDKN2A MUTATED                                          10
  CDKN2A WILD-TYPE                                        50
                  vv
clus               REGIONAL LYMPH NODE
  CDKN2A MUTATED                    24
  CDKN2A WILD-TYPE                 147
D3V4, multiclass
                                           clus
vv                                          CDKN2A MUTATED CDKN2A WILD-TYPE
  DISTANT METASTASIS                                     6               33
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               50
  REGIONAL LYMPH NODE                                   24              147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  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      21        7       22       13
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CDKN2A MUTATED           0         1         1         5          2
  CDKN2A WILD-TYPE        10        13         8        27         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CDKN2A MUTATED            5          8        3
  CDKN2A WILD-TYPE         18         38       13
D3V5, multiclass
             clus
vv            CDKN2A MUTATED CDKN2A WILD-TYPE
  I OR II NOS              3                7
  STAGE 0                  0                6
  STAGE I                  3               21
  STAGE IA                 3                7
  STAGE IB                 2               22
  STAGE II                 3               13
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                1                8
  STAGE III                5               27
  STAGE IIIA               2               11
  STAGE IIIB               5               18
  STAGE IIIC               8               38
  STAGE IV                 3               13
[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      11 10  9  5
  CDKN2A WILD-TYPE    41 49 45 52
D3V6, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1             11               41
  T2                10               49
  T3                 9               45
  T4                 5               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
  CDKN2A MUTATED    17  12   5   4
  CDKN2A WILD-TYPE 122  36  28  32
D3V7, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             17              122
  N1             12               36
  N2              5               28
  N3              4               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
  CDKN2A MUTATED    37   0   0   0   3
  CDKN2A WILD-TYPE 207   4   3   2   5
D3V8, multiclass
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  M0              37              207
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              3                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"
D3V9, binary
                  cls
clus                0  1
  CDKN2A MUTATED   10 13
  CDKN2A WILD-TYPE 93 55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     10   13
  CDKN2A WILD-TYPE   93   55
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              10               93
  YES             13               55
[1] 2 2
[1] FALSE
D3V10, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     6  35
  CDKN2A WILD-TYPE  30 204
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      6   35
  CDKN2A WILD-TYPE   30  204
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               6               30
  YES             35              204
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    17  24
  CDKN2A WILD-TYPE  89 146
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     17   24
  CDKN2A WILD-TYPE   89  146
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             17               89
  MALE               24              146
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       0                         0    41
  CDKN2A WILD-TYPE     3                         1   231
D3V13, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 41              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"
D3V14, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     0  41
  CDKN2A WILD-TYPE   3 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   41
  CDKN2A WILD-TYPE    3  228
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             41              228
[1] 2 2
[1] FALSE

Clustering(4) Variable = RPS27 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  RPS27 MUTATED    14   9
  RPS27 WILD-TYPE 112 131
  RPS27 MUTATED RPS27 WILD-TYPE 
             23             243 
  RPS27 MUTATED RPS27 WILD-TYPE 
              9             131 
$`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        15.85 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2GR 
       62.79         8.55         8.84        36.30        55.69         1.15 
TCGA-EE-A2MJ TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A193 
       63.42       122.73        51.62         3.22        22.22        31.40 
TCGA-FS-A1ZF TCGA-FS-A1ZK TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-RP-A694 
       11.08        12.89         0.13        11.61         0.69 

$`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        86.76        11.41        44.19 
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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31        60.23         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15        36.85         1.08        39.62         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        32.15         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        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        28.31        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-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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-A3AD 
       60.49        53.16        52.67         5.56       124.31         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        15.95        12.72        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14         0.95        27.35        18.41        21.73 
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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       19.53         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-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 
       14.70         5.79         0.33 

  RPS27 MUTATED RPS27 WILD-TYPE 
           0.13            0.16 
  RPS27 MUTATED RPS27 WILD-TYPE 
         122.73          125.65 
  RPS27 MUTATED RPS27 WILD-TYPE 
          15.85           17.33 
[1] "0.1 - 122.7 (15.8)" "0.2 - 125.7 (17.3)"
[1] "hr=" "1.5"
D4V2, survival
                 sevent
clus2               0   1
  RPS27 MUTATED    14   9
  RPS27 WILD-TYPE 115 132
  RPS27 MUTATED RPS27 WILD-TYPE 
             23             247 
  RPS27 MUTATED RPS27 WILD-TYPE 
              9             132 
$`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        91.56 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2GR 
       63.78        72.07        14.47        36.82       126.81        14.30 
TCGA-EE-A2MJ TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A193 
       96.23       122.73        51.62       172.18        53.19        31.40 
TCGA-FS-A1ZF TCGA-FS-A1ZK TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-RP-A694 
       15.45        23.93        47.54        11.74         0.69 

$`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        86.76        11.87        62.07 
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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
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 
       64.64         2.60        56.84        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       195.02        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        86.14        59.28        67.43       314.56       161.03 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       71.21        53.26       124.31         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      201.80        27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-A1ZG 
       27.72        48.85       357.37        53.52        40.27         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-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        22.92         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       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 
TCGA-RP-A693 
        0.33 

  RPS27 MUTATED RPS27 WILD-TYPE 
           0.69            0.16 
  RPS27 MUTATED RPS27 WILD-TYPE 
         172.18          357.37 
  RPS27 MUTATED RPS27 WILD-TYPE 
          53.19           51.35 
[1] "0.7 - 172.2 (53.2)" "0.2 - 357.4 (51.4)"
[1] "hr=" "1.2"
D4V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  RPS27 MUTATED                    6             1
  RPS27 WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RPS27 MUTATED                                           5                  11
  RPS27 WILD-TYPE                                        55                 160
D4V4, multiclass
                                           clus
vv                                          RPS27 MUTATED RPS27 WILD-TYPE
  DISTANT METASTASIS                                    6              33
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             5              55
  REGIONAL LYMPH NODE                                  11             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
  RPS27 MUTATED             0       1       1        0        2        3
  RPS27 WILD-TYPE          10       5      23       10       22       13
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RPS27 MUTATED           0         1         1         5          2          3
  RPS27 WILD-TYPE        10        13         8        27         11         20
                 vv
clus              STAGE IIIC STAGE IV
  RPS27 MUTATED            2        1
  RPS27 WILD-TYPE         44       15
D4V5, multiclass
             clus
vv            RPS27 MUTATED RPS27 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 1              23
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                3              13
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               5              27
  STAGE IIIA              2              11
  STAGE IIIB              3              20
  STAGE IIIC              2              44
  STAGE IV                1              15
[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    46 57 49 51
D4V6, multiclass
       clus
vv      RPS27 MUTATED RPS27 WILD-TYPE
  T0+T1             6              46
  T2                2              57
  T3                5              49
  T4                6              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
  RPS27 MUTATED    10   5   5   0
  RPS27 WILD-TYPE 129  43  28  36
D4V7, multiclass
    clus
vv   RPS27 MUTATED RPS27 WILD-TYPE
  N0            10             129
  N1             5              43
  N2             5              28
  N3             0              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               M0  M1 M1A M1B M1C
  RPS27 MUTATED    20   0   0   0   1
  RPS27 WILD-TYPE 224   4   3   2   7
D4V8, multiclass
     clus
vv    RPS27 MUTATED RPS27 WILD-TYPE
  M0             20             224
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             1               7
[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 96 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      7    3
  RPS27 WILD-TYPE   96   65
     clus
vv    RPS27 MUTATED RPS27 WILD-TYPE
  NO              7              96
  YES             3              65
[1] 2 2
[1] FALSE
D4V10, binary
                 cls
clus                0   1
  RPS27 MUTATED     7  16
  RPS27 WILD-TYPE  29 223
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      7   16
  RPS27 WILD-TYPE   29  223
     clus
vv    RPS27 MUTATED RPS27 WILD-TYPE
  NO              7              29
  YES            16             223
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, binary
                 cls
clus                0   1
  RPS27 MUTATED     7  16
  RPS27 WILD-TYPE  99 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      7   16
  RPS27 WILD-TYPE   99  154
        clus
vv       RPS27 MUTATED RPS27 WILD-TYPE
  FEMALE             7              99
  MALE              16             154
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPS27 MUTATED       0                         0    23
  RPS27 WILD-TYPE     3                         1   249
D4V13, multiclass
                           clus
vv                          RPS27 MUTATED RPS27 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                23             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"
D4V14, binary
                 cls
clus                0   1
  RPS27 MUTATED     0  23
  RPS27 WILD-TYPE   3 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS27 MUTATED      0   23
  RPS27 WILD-TYPE    3  246
                        clus
vv                       RPS27 MUTATED RPS27 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            23             246
[1] 2 2
[1] FALSE

Clustering(5) Variable = MRPS31 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  MRPS31 MUTATED     7  12
  MRPS31 WILD-TYPE 119 128
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              247 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              12              128 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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-A20I 
        5.13         4.31        60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        17.98        60.00        47.21        30.08 
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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
       44.25         7.96        63.42       125.65       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-A1ZQ 
        7.17        30.87        12.92        12.89        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  MRPS31 MUTATED MRPS31 WILD-TYPE 
            0.13             0.16 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
           56.02           125.65 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
           14.24            17.56 
[1] "0.1 - 56.0 (14.2)"  "0.2 - 125.7 (17.6)"
[1] "hr=" "1.4"
D5V2, survival
                  sevent
clus2                0   1
  MRPS31 MUTATED     7  12
  MRPS31 WILD-TYPE 122 129
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              19              251 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
              12              129 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56        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        63.78        72.07        64.64        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       96.23       158.63       203.05        47.54       248.65       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       109.58        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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  MRPS31 MUTATED MRPS31 WILD-TYPE 
            2.60             0.16 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
          204.66           357.37 
  MRPS31 MUTATED MRPS31 WILD-TYPE 
           53.16            51.62 
[1] "2.6 - 204.7 (53.2)" "0.2 - 357.4 (51.6)"
[1] "hr=" "1.3"
D5V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MRPS31 MUTATED                    5             1
  MRPS31 WILD-TYPE                 34             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MRPS31 MUTATED                                           2
  MRPS31 WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  MRPS31 MUTATED                    11
  MRPS31 WILD-TYPE                 160
D5V4, multiclass
                                           clus
vv                                          MRPS31 MUTATED MRPS31 WILD-TYPE
  DISTANT METASTASIS                                     5               34
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                   11              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
  MRPS31 MUTATED             0       0       3        1        0        1
  MRPS31 WILD-TYPE          10       6      21        9       24       15
                  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        30         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MRPS31 MUTATED            1          4        2
  MRPS31 WILD-TYPE         22         42       14
D5V5, multiclass
             clus
vv            MRPS31 MUTATED MRPS31 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  3               21
  STAGE IA                 1                9
  STAGE IB                 0               24
  STAGE II                 1               15
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               2               11
  STAGE IIIB               1               22
  STAGE IIIC               4               42
  STAGE IV                 2               14
[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    50 55 48 53
D5V6, multiclass
       clus
vv      MRPS31 MUTATED MRPS31 WILD-TYPE
  T0+T1              2               50
  T2                 4               55
  T3                 6               48
  T4                 4               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
  MRPS31 MUTATED     8   4   3   3
  MRPS31 WILD-TYPE 131  44  30  33
D5V7, multiclass
    clus
vv   MRPS31 MUTATED MRPS31 WILD-TYPE
  N0              8              131
  N1              4               44
  N2              3               30
  N3              3               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
  MRPS31 MUTATED    16   1   1   0   0
  MRPS31 WILD-TYPE 228   3   2   2   8
D5V8, multiclass
     clus
vv    MRPS31 MUTATED MRPS31 WILD-TYPE
  M0              16              228
  M1               1                3
  M1A              1                2
  M1B              0                2
  M1C              0                8
[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 99 62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      4    6
  MRPS31 WILD-TYPE   99   62
     clus
vv    MRPS31 MUTATED MRPS31 WILD-TYPE
  NO               4               99
  YES              6               62
[1] 2 2
[1] FALSE
D5V10, binary
                  cls
clus                 0   1
  MRPS31 MUTATED     2  17
  MRPS31 WILD-TYPE  34 222
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      2   17
  MRPS31 WILD-TYPE   34  222
     clus
vv    MRPS31 MUTATED MRPS31 WILD-TYPE
  NO               2               34
  YES             17              222
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, binary
                  cls
clus                 0   1
  MRPS31 MUTATED     5  14
  MRPS31 WILD-TYPE 101 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      5   14
  MRPS31 WILD-TYPE  101  156
        clus
vv       MRPS31 MUTATED MRPS31 WILD-TYPE
  FEMALE              5              101
  MALE               14              156
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MRPS31 MUTATED       0                         0    19
  MRPS31 WILD-TYPE     3                         1   253
D5V13, multiclass
                           clus
vv                          MRPS31 MUTATED MRPS31 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 19              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"
D5V14, binary
                  cls
clus                 0   1
  MRPS31 MUTATED     0  19
  MRPS31 WILD-TYPE   3 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS31 MUTATED      0   19
  MRPS31 WILD-TYPE    3  250
                        clus
vv                       MRPS31 MUTATED MRPS31 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             19              250
[1] 2 2
[1] FALSE

Clustering(6) Variable = NF1 MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    16  22
  NF1 WILD-TYPE 110 118
  NF1 MUTATED NF1 WILD-TYPE 
           38           228 
  NF1 MUTATED NF1 WILD-TYPE 
           22           118 
$`NF1 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A51R TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC 
       88.50        44.19        32.61        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        36.30        34.29        30.08        55.69 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
        1.15        14.56        63.42        53.16        52.67        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        86.76        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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 
       13.35        13.22        10.55         6.31        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        60.23        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W 
       39.62        12.03         8.09         8.84         9.99        32.15 
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        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        47.21        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46         2.73        44.25         7.96       125.65       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        60.49         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        51.62         3.68        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        0.95        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       12.95        38.40         5.72        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.80        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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.39         0.82        53.85        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        5.98         6.41         2.27         0.16        17.33         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.85        11.61        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  NF1 MUTATED NF1 WILD-TYPE 
         0.13          0.16 
  NF1 MUTATED NF1 WILD-TYPE 
        88.50        125.65 
  NF1 MUTATED NF1 WILD-TYPE 
        11.34         17.85 
[1] "0.1 - 88.5 (11.3)"  "0.2 - 125.7 (17.9)"
[1] "hr=" "1.4"
D6V2, survival
               sevent
clus2             0   1
  NF1 MUTATED    16  22
  NF1 WILD-TYPE 113 119
  NF1 MUTATED NF1 WILD-TYPE 
           38           232 
  NF1 MUTATED NF1 WILD-TYPE 
           22           119 
$`NF1 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A51R TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC 
      115.53        62.07        63.81        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        36.82        67.43        48.72       126.81 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
       14.30       204.66        96.23       162.48        71.21        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        86.76        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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25        54.02        17.29        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       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        63.78        72.07        64.64        56.84        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       195.02        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        86.14        59.28       314.56       161.03 
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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      103.20        16.96       158.63       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       134.40        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
      127.20        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
        9.17        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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       15.72       216.92        48.59       228.59       202.65        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-A1ZQ 
        9.70        32.75        47.38        23.93       101.26       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-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       77.88         0.16        19.30         9.90         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  NF1 MUTATED NF1 WILD-TYPE 
         0.20          0.16 
  NF1 MUTATED NF1 WILD-TYPE 
       204.66        357.37 
  NF1 MUTATED NF1 WILD-TYPE 
       42.245        53.175 
[1] "0.2 - 204.7 (42.2)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.5"
D6V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NF1 MUTATED                   10             1
  NF1 WILD-TYPE                 29             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NF1 MUTATED                                           9                  18
  NF1 WILD-TYPE                                        51                 153
D6V4, multiclass
                                           clus
vv                                          NF1 MUTATED NF1 WILD-TYPE
  DISTANT METASTASIS                                 10            29
  PRIMARY TUMOR                                       1             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           9            51
  REGIONAL LYMPH NODE                                18           153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               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      24        6       23       11
               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        27         11         21
               vv
clus            STAGE IIIC STAGE IV
  NF1 MUTATED            5        4
  NF1 WILD-TYPE         41       12
D6V5, multiclass
             clus
vv            NF1 MUTATED NF1 WILD-TYPE
  I OR II NOS           1             9
  STAGE 0               1             5
  STAGE I               0            24
  STAGE IA              4             6
  STAGE IB              1            23
  STAGE II              5            11
  STAGE IIA             2             8
  STAGE IIB             3            11
  STAGE IIC             0             9
  STAGE III             5            27
  STAGE IIIA            2            11
  STAGE IIIB            2            21
  STAGE IIIC            5            41
  STAGE IV              4            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
  NF1 MUTATED       5  3 10 11
  NF1 WILD-TYPE    47 56 44 46
D6V6, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  T0+T1           5            47
  T2              3            56
  T3             10            44
  T4             11            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
  NF1 MUTATED    23   6   4   3
  NF1 WILD-TYPE 116  42  29  33
D6V7, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0          23           116
  N1           6            42
  N2           4            29
  N3           3            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
  NF1 MUTATED    32   3   1   0   0
  NF1 WILD-TYPE 212   1   2   2   8
D6V8, multiclass
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  M0           32           212
  M1            3             1
  M1A           1             2
  M1B           0             2
  M1C           0             8
[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 89 59
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     14    9
  NF1 WILD-TYPE   89   59
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           14            89
  YES           9            59
[1] 2 2
[1] FALSE
D6V10, binary
               cls
clus              0   1
  NF1 MUTATED     6  32
  NF1 WILD-TYPE  30 207
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6   32
  NF1 WILD-TYPE   30  207
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            6            30
  YES          32           207
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, binary
               cls
clus              0   1
  NF1 MUTATED    11  27
  NF1 WILD-TYPE  95 143
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     11   27
  NF1 WILD-TYPE   95  143
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          11            95
  MALE            27           143
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED       0                         0    38
  NF1 WILD-TYPE     3                         1   234
D6V13, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              38           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"
D6V14, binary
               cls
clus              0   1
  NF1 MUTATED     1  35
  NF1 WILD-TYPE   2 234
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   35
  NF1 WILD-TYPE    2  234
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          35           234
[1] 2 2
[1] FALSE

Clustering(7) Variable = RAC1 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     9  11
  RAC1 WILD-TYPE 117 129
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            246 
  RAC1 MUTATED RAC1 WILD-TYPE 
            11            129 
$`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        32.61         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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         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 
       59.57       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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       54.74        31.30        54.31        32.28        21.44        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       52.01        47.87        13.68        17.72        23.11        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69         5.42 
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-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22         0.95        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07         6.58        17.72        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        47.38         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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       16.24        15.42        12.16        14.70         0.33         0.69 

  RAC1 MUTATED RAC1 WILD-TYPE 
          1.12           0.13 
  RAC1 MUTATED RAC1 WILD-TYPE 
        122.73         125.65 
  RAC1 MUTATED RAC1 WILD-TYPE 
         19.63          16.90 
[1] "1.1 - 122.7 (19.6)" "0.1 - 125.7 (16.9)"
[1] "hr=" "1"  
D7V2, survival
                sevent
clus2              0   1
  RAC1 MUTATED     9  11
  RAC1 WILD-TYPE 120 130
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            250 
  RAC1 MUTATED RAC1 WILD-TYPE 
            11            130 
$`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        63.81        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       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 
       59.57       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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       55.73        56.35       145.12        32.94        22.62        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
      101.26       133.55        11.41       148.80        53.16        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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.74       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         0.33         0.69 

  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         53.390 
[1] "6.7 - 122.7 (30.7)" "0.2 - 357.4 (53.4)"
[1] "hr=" "1.8"
D7V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  RAC1 MUTATED                    3             0
  RAC1 WILD-TYPE                 36             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RAC1 MUTATED                                           5                  12
  RAC1 WILD-TYPE                                        55                 159
D7V4, multiclass
                                           clus
vv                                          RAC1 MUTATED RAC1 WILD-TYPE
  DISTANT METASTASIS                                   3             36
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            5             55
  REGIONAL LYMPH NODE                                 12            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
  RAC1 MUTATED             0       0       1        0        1        3
  RAC1 WILD-TYPE          10       6      23       10       23       13
                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        29         12         22
                vv
clus             STAGE IIIC STAGE IV
  RAC1 MUTATED            6        0
  RAC1 WILD-TYPE         40       16
D7V5, multiclass
             clus
vv            RAC1 MUTATED RAC1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             23
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               3             13
  STAGE IIA              1              9
  STAGE IIB              0             14
  STAGE IIC              2              7
  STAGE III              3             29
  STAGE IIIA             1             12
  STAGE IIIB             1             22
  STAGE IIIC             6             40
  STAGE IV               0             16
[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    48 57 49 52
D7V6, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  T0+T1            4             48
  T2               2             57
  T3               5             49
  T4               5             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
  RAC1 MUTATED     8   2   4   5
  RAC1 WILD-TYPE 131  46  29  31
D7V7, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  N0            8            131
  N1            2             46
  N2            4             29
  N3            5             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
  RAC1 MUTATED    19   0   0   0   0
  RAC1 WILD-TYPE 225   4   3   2   8
D7V8, multiclass
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  M0            19            225
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 99 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      4    5
  RAC1 WILD-TYPE   99   63
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             4             99
  YES            5             63
[1] 2 2
[1] FALSE
D7V10, binary
                cls
clus               0   1
  RAC1 MUTATED     6  14
  RAC1 WILD-TYPE  30 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      6   14
  RAC1 WILD-TYPE   30  225
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             6             30
  YES           14            225
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, binary
                cls
clus               0   1
  RAC1 MUTATED     6  14
  RAC1 WILD-TYPE 100 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      6   14
  RAC1 WILD-TYPE  100  156
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            6            100
  MALE             14            156
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED       0                         0    20
  RAC1 WILD-TYPE     3                         1   252
D7V13, multiclass
                           clus
vv                          RAC1 MUTATED RAC1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               20            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"
D7V14, binary
                cls
clus               0   1
  RAC1 MUTATED     0  20
  RAC1 WILD-TYPE   3 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0   20
  RAC1 WILD-TYPE    3  249
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           20            249
[1] 2 2
[1] FALSE

Clustering(8) Variable = ARID2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    13  21
  ARID2 WILD-TYPE 113 119
  ARID2 MUTATED ARID2 WILD-TYPE 
             34             232 
  ARID2 MUTATED ARID2 WILD-TYPE 
             21             119 
$`ARID2 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GR TCGA-D3-A5GU 
       44.19        64.44         6.31       103.59        13.68        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        36.30        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        51.62        13.81        15.95        18.41        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        86.76        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        59.57 
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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       25.78        52.01        47.87        17.72         4.01        21.93 
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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       36.85         1.08        39.62         8.09         8.84         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
       32.15         8.09        11.31        49.22         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL 
       51.12        34.29        60.00        47.21        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        55.69         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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       60.49        53.16        52.67         5.56       124.31       122.73 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        27.35        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.30         3.39        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-A4F0 TCGA-FS-A4F4 
       40.64         8.68        27.39         0.82        53.85         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  ARID2 MUTATED ARID2 WILD-TYPE 
           0.99            0.13 
  ARID2 MUTATED ARID2 WILD-TYPE 
         103.59          125.65 
  ARID2 MUTATED ARID2 WILD-TYPE 
         14.025          17.640 
[1] "1.0 - 103.6 (14.0)" "0.1 - 125.7 (17.6)"
[1] "hr=" "1.3"
D8V2, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    13  21
  ARID2 WILD-TYPE 116 120
  ARID2 MUTATED ARID2 WILD-TYPE 
             34             236 
  ARID2 MUTATED ARID2 WILD-TYPE 
             21             120 
$`ARID2 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GR TCGA-D3-A5GU 
       62.07        66.08        13.87       103.59       178.32       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        36.82       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        51.62        13.81        23.47        51.35        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        86.76        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        59.57 
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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
       26.89       135.75       137.92        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.84        37.35        14.47        25.87       195.02        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        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      161.03       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 
      126.81        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-A2MF 
       21.67       129.27        28.83        19.76       103.27       268.73 
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       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       124.31       122.73         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19       201.80        27.35       109.58       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-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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-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-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.09        77.82        66.67       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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ARID2 MUTATED ARID2 WILD-TYPE 
          10.13            0.16 
  ARID2 MUTATED ARID2 WILD-TYPE 
         357.37          268.93 
  ARID2 MUTATED ARID2 WILD-TYPE 
         50.400          53.175 
[1] "10.1 - 357.4 (50.4)" "0.2 - 268.9 (53.2)" 
[1] "hr=" "1.1"
D8V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ARID2 MUTATED                    6             1
  ARID2 WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ARID2 MUTATED                                          10                  18
  ARID2 WILD-TYPE                                        50                 153
D8V4, multiclass
                                           clus
vv                                          ARID2 MUTATED ARID2 WILD-TYPE
  DISTANT METASTASIS                                    6              33
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            10              50
  REGIONAL LYMPH NODE                                  18             153
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 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      23        7       21       14
                 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        27         11         21
                 vv
clus              STAGE IIIC STAGE IV
  ARID2 MUTATED            5        1
  ARID2 WILD-TYPE         41       15
D8V5, multiclass
             clus
vv            ARID2 MUTATED ARID2 WILD-TYPE
  I OR II NOS             3               7
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                3               7
  STAGE IB                3              21
  STAGE II                2              14
  STAGE IIA               3               7
  STAGE IIB               3              11
  STAGE IIC               1               8
  STAGE III               5              27
  STAGE IIIA              2              11
  STAGE IIIB              2              21
  STAGE IIIC              5              41
  STAGE IV                1              15
[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    43 54 43 53
D8V6, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  T0+T1             9              43
  T2                5              54
  T3               11              43
  T4                4              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
  ARID2 MUTATED    20   6   6   2
  ARID2 WILD-TYPE 119  42  27  34
D8V7, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            20             119
  N1             6              42
  N2             6              27
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  ARID2 MUTATED    33   1   0   0   0
  ARID2 WILD-TYPE 211   3   3   2   8
D8V8, multiclass
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  M0             33             211
  M1              1               3
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 90 58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     13   10
  ARID2 WILD-TYPE   90   58
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             13              90
  YES            10              58
[1] 2 2
[1] FALSE
D8V10, binary
                 cls
clus                0   1
  ARID2 MUTATED     6  29
  ARID2 WILD-TYPE  30 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      6   29
  ARID2 WILD-TYPE   30  210
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO              6              30
  YES            29             210
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, binary
                 cls
clus                0   1
  ARID2 MUTATED    13  22
  ARID2 WILD-TYPE  93 148
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     13   22
  ARID2 WILD-TYPE   93  148
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            13              93
  MALE              22             148
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED       0                         0    35
  ARID2 WILD-TYPE     3                         1   237
D8V13, multiclass
                           clus
vv                          ARID2 MUTATED ARID2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                35             237
[1] 3 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   2 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   34
  ARID2 WILD-TYPE    2  235
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            34             235
[1] 2 2
[1] FALSE

Clustering(9) Variable = C15ORF23 MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                  0   1
  C15ORF23 MUTATED     9  10
  C15ORF23 WILD-TYPE 117 130
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                19                247 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                10                130 
$`C15ORF23 MUTATED`
TCGA-D3-A2JD TCGA-D3-A51E TCGA-D3-A5GO TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29G 
       11.41        93.21        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 
       36.30        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-GF-A6C9 
       22.92        21.60        40.64        10.78         7.23        11.61 
TCGA-GN-A266 
       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        86.76        44.19 
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 
       59.57       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        29.23        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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 
       60.23         4.34        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        11.15        62.79        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       36.33        51.12        60.00        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        55.69         5.42 
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-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        21.60        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       15.95         3.22        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-A4FB 
        5.23        53.85         7.36        28.73        14.20         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 
       17.33         9.90         0.85        44.28        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
              1.12               0.13 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             93.21             125.65 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             12.72              17.33 
[1] "1.1 - 93.2 (12.7)"  "0.1 - 125.7 (17.3)"
[1] "hr=" "1.1"
D9V2, survival
                    sevent
clus2                  0   1
  C15ORF23 MUTATED     9  10
  C15ORF23 WILD-TYPE 120 131
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                19                251 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                10                131 
$`C15ORF23 MUTATED`
TCGA-D3-A2JD TCGA-D3-A51E TCGA-D3-A5GO TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29G 
       11.87       174.84       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 
       36.82        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-GF-A6C9 
      127.20        36.95        53.16        12.43         7.23        11.74 
TCGA-GN-A266 
       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        86.76        62.07 
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 
       59.57       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        45.30        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       135.75       178.32        18.18 
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 
       22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        63.78        64.64         2.60        56.84        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       195.02 
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        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       203.05       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       51.62         3.68        54.51        13.81        23.47       172.18 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        26.56        49.48        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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
              7.23               0.16 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
            314.56             357.37 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             53.16              51.62 
[1] "7.2 - 314.6 (53.2)" "0.2 - 357.4 (51.6)"
[1] "hr=" "1.2"
D9V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  C15ORF23 MUTATED                    3             0
  C15ORF23 WILD-TYPE                 36             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C15ORF23 MUTATED                                           7
  C15ORF23 WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  C15ORF23 MUTATED                     9
  C15ORF23 WILD-TYPE                 162
D9V4, multiclass
                                           clus
vv                                          C15ORF23 MUTATED C15ORF23 WILD-TYPE
  DISTANT METASTASIS                                       3                 36
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 53
  REGIONAL LYMPH NODE                                      9                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
  C15ORF23 MUTATED             1       0       2        0        0        4
  C15ORF23 WILD-TYPE           9       6      22       10       24       12
                    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        30         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C15ORF23 MUTATED            2          4        0
  C15ORF23 WILD-TYPE         21         42       16
D9V5, multiclass
             clus
vv            C15ORF23 MUTATED C15ORF23 WILD-TYPE
  I OR II NOS                1                  9
  STAGE 0                    0                  6
  STAGE I                    2                 22
  STAGE IA                   0                 10
  STAGE IB                   0                 24
  STAGE II                   4                 12
  STAGE IIA                  0                 10
  STAGE IIB                  2                 12
  STAGE IIC                  0                  9
  STAGE III                  2                 30
  STAGE IIIA                 1                 12
  STAGE IIIB                 2                 21
  STAGE IIIC                 4                 42
  STAGE IV                   0                 16
[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       1  4  5  7
  C15ORF23 WILD-TYPE    51 55 49 50
D9V6, multiclass
       clus
vv      C15ORF23 MUTATED C15ORF23 WILD-TYPE
  T0+T1                1                 51
  T2                   4                 55
  T3                   5                 49
  T4                   7                 50
[1] 4 2
[1] TRUE
[1] "dimension of 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   2
  C15ORF23 WILD-TYPE 130  44  31  34
D9V7, multiclass
    clus
vv   C15ORF23 MUTATED C15ORF23 WILD-TYPE
  N0                9                130
  N1                4                 44
  N2                2                 31
  N3                2                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  C15ORF23 MUTATED    17   0   0   0   0
  C15ORF23 WILD-TYPE 227   4   3   2   8
D9V8, multiclass
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  M0                17                227
  M1                 0                  4
  M1A                0                  3
  M1B                0                  2
  M1C                0                  8
[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 98 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      5    6
  C15ORF23 WILD-TYPE   98   62
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  NO                 5                 98
  YES                6                 62
[1] 2 2
[1] FALSE
D9V10, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     3  16
  C15ORF23 WILD-TYPE  33 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      3   16
  C15ORF23 WILD-TYPE   33  223
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  NO                 3                 33
  YES               16                223
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     5  14
  C15ORF23 WILD-TYPE 101 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      5   14
  C15ORF23 WILD-TYPE  101  156
        clus
vv       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  FEMALE                5                101
  MALE                 14                156
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C15ORF23 MUTATED       0                         0    19
  C15ORF23 WILD-TYPE     3                         1   253
D9V13, multiclass
                           clus
vv                          C15ORF23 MUTATED C15ORF23 WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   19                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"
D9V14, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     0  19
  C15ORF23 WILD-TYPE   3 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      0   19
  C15ORF23 WILD-TYPE    3  250
                        clus
vv                       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               19                250
[1] 2 2
[1] FALSE

Clustering(10) Variable = PTEN MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    12  11
  PTEN WILD-TYPE 114 129
  PTEN MUTATED PTEN WILD-TYPE 
            23            243 
  PTEN MUTATED PTEN WILD-TYPE 
            11            129 
$`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 
       25.78        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        18.41        11.90         4.21 
TCGA-ER-A2NE TCGA-ER-A42K TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FW-A3I3 
        1.51         5.62        15.72         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        86.76        11.41        44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR 
       54.31        32.28        21.44        32.61        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         1.08        39.62         9.50         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 
       28.31        55.69         5.42         1.15        34.98         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19F 
        5.72        76.41        25.18         3.78         3.52        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      114.15        34.88        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.87        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX 
       22.49         1.71        18.41        85.74        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-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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  PTEN MUTATED PTEN WILD-TYPE 
          0.20           0.13 
  PTEN MUTATED PTEN WILD-TYPE 
        111.09         125.65 
  PTEN MUTATED PTEN WILD-TYPE 
         13.02          17.72 
[1] "0.2 - 111.1 (13.0)" "0.1 - 125.7 (17.7)"
[1] "hr=" "1"  
D10V2, survival
                sevent
clus2              0   1
  PTEN MUTATED    12  11
  PTEN WILD-TYPE 117 130
  PTEN MUTATED PTEN WILD-TYPE 
            23            247 
  PTEN MUTATED PTEN WILD-TYPE 
            11            130 
$`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 
       26.89       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        51.35        13.02         6.44 
TCGA-ER-A2NE TCGA-ER-A42K TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FW-A3I3 
       20.15         6.77        15.72        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        86.76        11.87        62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR 
      145.12        32.94        22.62        63.81       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       56.84        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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        27.35       109.58       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-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        26.37       268.93       152.35 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        23.34        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-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       92.98       174.21       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-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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  PTEN MUTATED PTEN WILD-TYPE 
          0.20           0.16 
  PTEN MUTATED PTEN WILD-TYPE 
        138.81         357.37 
  PTEN MUTATED PTEN WILD-TYPE 
         55.59          50.89 
[1] "0.2 - 138.8 (55.6)" "0.2 - 357.4 (50.9)"
[1] "hr=" "1.2"
D10V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  PTEN MUTATED                    2             1
  PTEN WILD-TYPE                 37             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PTEN MUTATED                                           4                  16
  PTEN WILD-TYPE                                        56                 155
D10V4, multiclass
                                           clus
vv                                          PTEN MUTATED PTEN WILD-TYPE
  DISTANT METASTASIS                                   2             37
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             56
  REGIONAL LYMPH NODE                                 16            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
  PTEN MUTATED             0       1       1        1        5        1
  PTEN WILD-TYPE          10       5      23        9       19       15
                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        31         12         22
                vv
clus             STAGE IIIC STAGE IV
  PTEN MUTATED            5        2
  PTEN WILD-TYPE         41       14
D10V5, multiclass
             clus
vv            PTEN MUTATED PTEN WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                1             23
  STAGE IA               1              9
  STAGE IB               5             19
  STAGE II               1             15
  STAGE IIA              2              8
  STAGE IIB              1             13
  STAGE IIC              1              8
  STAGE III              1             31
  STAGE IIIA             1             12
  STAGE IIIB             1             22
  STAGE IIIC             5             41
  STAGE IV               2             14
[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  6
  PTEN WILD-TYPE    48 52 51 51
D10V6, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            4             48
  T2               7             52
  T3               3             51
  T4               6             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
  PTEN MUTATED    14   5   1   3
  PTEN WILD-TYPE 125  43  32  33
D10V7, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           14            125
  N1            5             43
  N2            1             32
  N3            3             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
  PTEN MUTATED    20   2   0   0   0
  PTEN WILD-TYPE 224   2   3   2   8
D10V8, multiclass
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  M0            20            224
  M1             2              2
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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  8
  PTEN WILD-TYPE 94 60
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      9    8
  PTEN WILD-TYPE   94   60
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             9             94
  YES            8             60
[1] 2 2
[1] FALSE
D10V10, binary
                cls
clus               0   1
  PTEN MUTATED     4  18
  PTEN WILD-TYPE  32 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4   18
  PTEN WILD-TYPE   32  221
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             4             32
  YES           18            221
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, binary
                cls
clus               0   1
  PTEN MUTATED    13  10
  PTEN WILD-TYPE  93 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     13   10
  PTEN WILD-TYPE   93  160
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           13             93
  MALE             10            160
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0    23
  PTEN WILD-TYPE     3                         1   249
D10V13, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               23            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"
D10V14, binary
                cls
clus               0   1
  PTEN MUTATED     0  23
  PTEN WILD-TYPE   3 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   23
  PTEN WILD-TYPE    3  246
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           23            246
[1] 2 2
[1] FALSE

Clustering(11) Variable = NOTCH2NL MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                  0   1
  NOTCH2NL MUTATED     7   8
  NOTCH2NL WILD-TYPE 119 132
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                251 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 8                132 
$`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        62.79         8.09 
TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A3AB TCGA-EE-A3AG 
       51.12        55.69         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        86.76        11.41        44.19         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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         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        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        1.08        39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        36.33        34.29        17.98        60.00        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-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-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31        51.62         3.68        30.15        13.81 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        14.24         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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         6.41         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
              2.27               0.13 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            122.73             125.65 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             15.95              17.33 
[1] "2.3 - 122.7 (15.9)" "0.1 - 125.7 (17.3)"
[1] "hr=" "1.1"
D11V2, survival
                    sevent
clus2                  0   1
  NOTCH2NL MUTATED     7   8
  NOTCH2NL WILD-TYPE 122 133
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                15                255 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 8                133 
$`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        63.78        37.35 
TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A3AB TCGA-EE-A3AG 
       59.28       126.81        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        86.76        11.87        62.07       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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        64.64         2.60        56.84 
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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         3.68        54.51        13.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             13.91               0.16 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            138.81             357.37 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             63.78              51.35 
[1] "13.9 - 138.8 (63.8)" "0.2 - 357.4 (51.4)" 
[1] "hr=" "1.1"
D11V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  NOTCH2NL MUTATED                    1             0
  NOTCH2NL WILD-TYPE                 38             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  NOTCH2NL MUTATED                                           5
  NOTCH2NL WILD-TYPE                                        55
                    vv
clus                 REGIONAL LYMPH NODE
  NOTCH2NL MUTATED                     9
  NOTCH2NL WILD-TYPE                 162
D11V4, multiclass
                                           clus
vv                                          NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  DISTANT METASTASIS                                       1                 38
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                5                 55
  REGIONAL LYMPH NODE                                      9                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
  NOTCH2NL MUTATED             0       0       2        0        2        2
  NOTCH2NL WILD-TYPE          10       6      22       10       22       14
                    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        28         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  NOTCH2NL MUTATED            3          1        0
  NOTCH2NL WILD-TYPE         20         45       16
D11V5, multiclass
             clus
vv            NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    2                 22
  STAGE IA                   0                 10
  STAGE IB                   2                 22
  STAGE II                   2                 14
  STAGE IIA                  0                 10
  STAGE IIB                  1                 13
  STAGE IIC                  0                  9
  STAGE III                  4                 28
  STAGE IIIA                 0                 13
  STAGE IIIB                 3                 20
  STAGE IIIC                 1                 45
  STAGE IV                   0                 16
[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    48 54 50 55
D11V6, multiclass
       clus
vv      NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  T0+T1                4                 48
  T2                   5                 54
  T3                   4                 50
  T4                   2                 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
  NOTCH2NL MUTATED     7   5   2   1
  NOTCH2NL WILD-TYPE 132  43  31  35
D11V7, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  N0                7                132
  N1                5                 43
  N2                2                 31
  N3                1                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  NOTCH2NL MUTATED    15   0   0   0   0
  NOTCH2NL WILD-TYPE 229   4   3   2   8
D11V8, multiclass
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  M0                15                229
  M1                 0                  4
  M1A                0                  3
  M1B                0                  2
  M1C                0                  8
[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 96 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      7    3
  NOTCH2NL WILD-TYPE   96   65
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  NO                 7                 96
  YES                3                 65
[1] 2 2
[1] FALSE
D11V10, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     3  12
  NOTCH2NL WILD-TYPE  33 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      3   12
  NOTCH2NL WILD-TYPE   33  227
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  NO                 3                 33
  YES               12                227
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     3  12
  NOTCH2NL WILD-TYPE 103 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      3   12
  NOTCH2NL WILD-TYPE  103  158
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  FEMALE                3                103
  MALE                 12                158
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2NL MUTATED       0                         0    15
  NOTCH2NL WILD-TYPE     3                         1   257
D11V13, multiclass
                           clus
vv                          NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   15                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"
D11V14, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     0  15
  NOTCH2NL WILD-TYPE   3 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      0   15
  NOTCH2NL WILD-TYPE    3  254
                        clus
vv                       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               15                254
[1] 2 2
[1] FALSE

Clustering(12) Variable = MAP2K1 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     8   3
  MAP2K1 WILD-TYPE 118 137
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              11              255 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               3              137 
$`MAP2K1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-D3-A51F TCGA-EB-A5UN TCGA-EE-A29M 
       70.16        28.08        29.23        54.74        13.22        39.62 
TCGA-EE-A29R TCGA-EE-A2M5 TCGA-EE-A2MU TCGA-EE-A3JB TCGA-EE-A3JH 
        8.84         8.84         5.56         0.95        21.73 

$`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        86.76        11.41        44.19         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        59.57 
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 
       93.21        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       25.78        52.01        47.87        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        4.01        21.93         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-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        19.00        13.35        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 
       60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
        1.08         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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         5.42         1.15        13.02        34.98        36.33 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67       124.31       122.73        51.62         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        18.41 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
            0.95             0.13 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           70.16           125.65 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           21.73            16.47 
[1] "0.9 - 70.2 (21.7)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "2"  
D12V2, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     9   3
  MAP2K1 WILD-TYPE 120 138
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              12              258 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               3              138 
$`MAP2K1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-D3-A51F TCGA-D9-A149 TCGA-EB-A5UN 
       71.80        28.08        45.30        55.73        54.67        52.01 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A2M5 TCGA-EE-A2MU TCGA-EE-A3JB TCGA-EE-A3JH 
       56.84        14.47        21.67        53.26       201.80       109.58 

$`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        86.76        11.87        62.07       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        59.57 
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 
      174.84        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29 
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       133.81       151.27        91.56 
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 
       63.78        72.07        64.64         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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      248.65        43.23       134.40       162.48        71.21       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JI TCGA-ER-A193 TCGA-ER-A195 
       53.19        27.35        51.35       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           14.47             0.16 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          201.80           357.37 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          53.965           51.120 
[1] "14.5 - 201.8 (54.0)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "2"  
D12V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MAP2K1 MUTATED                    1             0
  MAP2K1 WILD-TYPE                 38             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MAP2K1 MUTATED                                           5
  MAP2K1 WILD-TYPE                                        55
                  vv
clus               REGIONAL LYMPH NODE
  MAP2K1 MUTATED                     6
  MAP2K1 WILD-TYPE                 165
D12V4, multiclass
                                           clus
vv                                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  DISTANT METASTASIS                                     1               38
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              5               55
  REGIONAL LYMPH NODE                                    6              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
  MAP2K1 MUTATED             0       0       1        1        2        0
  MAP2K1 WILD-TYPE          10       6      23        9       22       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MAP2K1 MUTATED           0         0         1         2          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         22         44       15
D12V5, multiclass
             clus
vv            MAP2K1 MUTATED MAP2K1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 0               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                1                8
  STAGE III                2               30
  STAGE IIIA               0               13
  STAGE IIIB               1               22
  STAGE IIIC               2               44
  STAGE IV                 1               15
[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  2  3
  MAP2K1 WILD-TYPE    50 55 52 54
D12V6, multiclass
       clus
vv      MAP2K1 MUTATED MAP2K1 WILD-TYPE
  T0+T1              2               50
  T2                 4               55
  T3                 2               52
  T4                 3               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
  MAP2K1 MUTATED     4   5   1   1
  MAP2K1 WILD-TYPE 135  43  32  35
D12V7, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  N0              4              135
  N1              5               43
  N2              1               32
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  MAP2K1 MUTATED    11   0   0   1   0
  MAP2K1 WILD-TYPE 233   4   3   1   8
D12V8, multiclass
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  M0              11              233
  M1               0                4
  M1A              0                3
  M1B              1                1
  M1C              0                8
[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 99 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      4    4
  MAP2K1 WILD-TYPE   99   64
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               4               99
  YES              4               64
[1] 2 2
[1] FALSE
D12V10, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     1  11
  MAP2K1 WILD-TYPE  35 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      1   11
  MAP2K1 WILD-TYPE   35  228
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               1               35
  YES             11              228
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     5   7
  MAP2K1 WILD-TYPE 101 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      5    7
  MAP2K1 WILD-TYPE  101  163
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  FEMALE              5              101
  MALE                7              163
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP2K1 MUTATED       0                         0    12
  MAP2K1 WILD-TYPE     3                         1   260
D12V13, multiclass
                           clus
vv                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 12              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"
D12V14, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     0  12
  MAP2K1 WILD-TYPE   3 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      0   12
  MAP2K1 WILD-TYPE    3  257
                        clus
vv                       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             12              257
[1] 2 2
[1] FALSE

Clustering(13) Variable = PPP6C MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  PPP6C MUTATED    13   7
  PPP6C WILD-TYPE 113 133
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             246 
  PPP6C MUTATED PPP6C WILD-TYPE 
              7             133 
$`PPP6C MUTATED`
TCGA-D3-A3C8 TCGA-D3-A3MV TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-DA-A3F8 
       46.32        29.23        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 
       23.15         1.08         8.84        32.15        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL 
       19.36         7.00        13.15         0.20        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.09         9.99         2.43         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      125.65        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A1ZJ 
        3.39         8.22        19.53        11.08         7.17        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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64         8.68         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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  PPP6C MUTATED PPP6C WILD-TYPE 
           0.99            0.13 
  PPP6C MUTATED PPP6C WILD-TYPE 
         111.91          125.65 
  PPP6C MUTATED PPP6C WILD-TYPE 
          25.27           15.90 
[1] "1.0 - 111.9 (25.3)" "0.1 - 125.7 (15.9)"
[1] "hr=" "1.8"
D13V2, survival
                 sevent
clus2               0   1
  PPP6C MUTATED    13   7
  PPP6C WILD-TYPE 116 134
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             250 
  PPP6C MUTATED PPP6C WILD-TYPE 
              7             134 
$`PPP6C MUTATED`
TCGA-D3-A3C8 TCGA-D3-A3MV TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-DA-A3F8 
       46.32        45.30        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 
       68.25         2.60        14.47       195.02       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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64        56.84        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        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28        67.43       161.03       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       126.81 
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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
      103.20        16.96       204.66        96.23       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-A1ZD 
       20.91        28.08         7.79        27.72        48.85        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27        15.45         9.70        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-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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        10.13        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  PPP6C MUTATED PPP6C WILD-TYPE 
           2.60            0.16 
  PPP6C MUTATED PPP6C WILD-TYPE 
         357.37          268.93 
  PPP6C MUTATED PPP6C WILD-TYPE 
          67.25           51.12 
[1] "2.6 - 357.4 (67.2)" "0.2 - 268.9 (51.1)"
[1] "hr=" "3.6"
D13V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PPP6C MUTATED                    1             1
  PPP6C WILD-TYPE                 38             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PPP6C MUTATED                                           5                  13
  PPP6C WILD-TYPE                                        55                 158
D13V4, multiclass
                                           clus
vv                                          PPP6C MUTATED PPP6C WILD-TYPE
  DISTANT METASTASIS                                    1              38
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             5              55
  REGIONAL LYMPH NODE                                  13             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
  PPP6C MUTATED             1       1       2        0        0        1
  PPP6C WILD-TYPE           9       5      22       10       24       15
                 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        31         11         20
                 vv
clus              STAGE IIIC STAGE IV
  PPP6C MUTATED            5        1
  PPP6C WILD-TYPE         41       15
D13V5, multiclass
             clus
vv            PPP6C MUTATED PPP6C WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 1               5
  STAGE I                 2              22
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               1              31
  STAGE IIIA              2              11
  STAGE IIIB              3              20
  STAGE IIIC              5              41
  STAGE IV                1              15
[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    49 55 50 53
D13V6, multiclass
       clus
vv      PPP6C MUTATED PPP6C WILD-TYPE
  T0+T1             3              49
  T2                4              55
  T3                4              50
  T4                4              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
  PPP6C MUTATED     7   4   4   4
  PPP6C WILD-TYPE 132  44  29  32
D13V7, multiclass
    clus
vv   PPP6C MUTATED PPP6C WILD-TYPE
  N0             7             132
  N1             4              44
  N2             4              29
  N3             4              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
  PPP6C MUTATED    18   0   0   0   1
  PPP6C WILD-TYPE 226   4   3   2   7
D13V8, multiclass
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  M0             18             226
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             1               7
[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 96 61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      7    7
  PPP6C WILD-TYPE   96   61
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  NO              7              96
  YES             7              61
[1] 2 2
[1] FALSE
D13V10, binary
                 cls
clus                0   1
  PPP6C MUTATED     1  19
  PPP6C WILD-TYPE  35 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      1   19
  PPP6C WILD-TYPE   35  220
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  NO              1              35
  YES            19             220
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, binary
                 cls
clus                0   1
  PPP6C MUTATED     8  12
  PPP6C WILD-TYPE  98 158
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      8   12
  PPP6C WILD-TYPE   98  158
        clus
vv       PPP6C MUTATED PPP6C WILD-TYPE
  FEMALE             8              98
  MALE              12             158
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP6C MUTATED       0                         0    20
  PPP6C WILD-TYPE     3                         1   252
D13V13, multiclass
                           clus
vv                          PPP6C MUTATED PPP6C WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                20             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"
D13V14, binary
                 cls
clus                0   1
  PPP6C MUTATED     0  20
  PPP6C WILD-TYPE   3 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      0   20
  PPP6C WILD-TYPE    3  249
                        clus
vv                       PPP6C MUTATED PPP6C WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            20             249
[1] 2 2
[1] FALSE

Clustering(14) Variable = IDH1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     5   8
  IDH1 WILD-TYPE 121 132
  IDH1 MUTATED IDH1 WILD-TYPE 
            13            253 
  IDH1 MUTATED IDH1 WILD-TYPE 
             8            132 
$`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 
TCGA-RP-A693 
        0.33 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       13.68        17.72        23.11        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        9.21         1.18        37.97        11.15        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         1.08        39.62         9.50         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         5.42         1.15        13.02 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
        3.22        22.92        21.60        21.60        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       12.62        11.74         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 
TCGA-RP-A694 
        0.69 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.33           0.13 
  IDH1 MUTATED IDH1 WILD-TYPE 
         52.08         125.65 
  IDH1 MUTATED IDH1 WILD-TYPE 
         15.42          17.56 
[1] "0.3 - 52.1 (15.4)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.3"
D14V2, survival
                sevent
clus2              0   1
  IDH1 MUTATED     6   8
  IDH1 WILD-TYPE 123 133
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            256 
  IDH1 MUTATED IDH1 WILD-TYPE 
             8            133 
$`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 TCGA-RP-A693 
       62.79         0.33 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      178.32        18.18       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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64         2.60        56.84 
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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET 
       23.34        20.15        16.37        31.27        32.05        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       32.48        39.58         6.67         0.69 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.33           0.16 
  IDH1 MUTATED IDH1 WILD-TYPE 
        247.04         357.37 
  IDH1 MUTATED IDH1 WILD-TYPE 
        63.070         50.825 
[1] "0.3 - 247.0 (63.1)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1"  
D14V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  IDH1 MUTATED                    6             0
  IDH1 WILD-TYPE                 33             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  IDH1 MUTATED                                           2                   7
  IDH1 WILD-TYPE                                        58                 164
D14V4, multiclass
                                           clus
vv                                          IDH1 MUTATED IDH1 WILD-TYPE
  DISTANT METASTASIS                                   6             33
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            2             58
  REGIONAL LYMPH NODE                                  7            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
  IDH1 MUTATED             0       0       1        1        0        2
  IDH1 WILD-TYPE          10       6      23        9       24       14
                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        32         11         23
                vv
clus             STAGE IIIC STAGE IV
  IDH1 MUTATED            1        2
  IDH1 WILD-TYPE         45       14
D14V5, multiclass
             clus
vv            IDH1 MUTATED IDH1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             23
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               2             14
  STAGE IIA              1              9
  STAGE IIB              2             12
  STAGE IIC              1              8
  STAGE III              0             32
  STAGE IIIA             2             11
  STAGE IIIB             0             23
  STAGE IIIC             1             45
  STAGE IV               2             14
[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    51 57 50 53
D14V6, multiclass
       clus
vv      IDH1 MUTATED IDH1 WILD-TYPE
  T0+T1            1             51
  T2               2             57
  T3               4             50
  T4               4             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
  IDH1 MUTATED     8   3   0   1
  IDH1 WILD-TYPE 131  45  33  35
D14V7, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  N0            8            131
  N1            3             45
  N2            0             33
  N3            1             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  IDH1 MUTATED    12   0   0   0   2
  IDH1 WILD-TYPE 232   4   3   2   6
D14V8, multiclass
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  M0            12            232
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            2              6
[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 96 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      7    2
  IDH1 WILD-TYPE   96   66
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             7             96
  YES            2             66
[1] 2 2
[1] FALSE
D14V10, binary
                cls
clus               0   1
  IDH1 MUTATED     1  14
  IDH1 WILD-TYPE  35 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      1   14
  IDH1 WILD-TYPE   35  225
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             1             35
  YES           14            225
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, binary
                cls
clus               0   1
  IDH1 MUTATED     4  11
  IDH1 WILD-TYPE 102 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      4   11
  IDH1 WILD-TYPE  102  159
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            4            102
  MALE             11            159
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         0    15
  IDH1 WILD-TYPE     3                         1   257
D14V13, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               15            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"
D14V14, binary
                cls
clus               0   1
  IDH1 MUTATED     0  14
  IDH1 WILD-TYPE   3 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   14
  IDH1 WILD-TYPE    3  255
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           14            255
[1] 2 2
[1] FALSE

Clustering(15) Variable = PDE1A MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  PDE1A MUTATED    18  21
  PDE1A WILD-TYPE 108 119
  PDE1A MUTATED PDE1A WILD-TYPE 
             39             227 
  PDE1A MUTATED PDE1A WILD-TYPE 
             21             119 
$`PDE1A MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1IC 
       44.19        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        62.79 
TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GE 
       39.62         9.99        11.31        36.30        34.29        60.00 
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        60.49 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19F 
       52.67        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 TCGA-RP-A693 
        0.13        84.72         0.33 

$`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        86.76        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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       23.11        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        1.18         7.99        37.97         8.55        36.85         1.08 
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        32.15 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
        8.09        49.22         9.67        36.33        51.12        17.98 
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-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       55.69         5.42         1.15        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70        47.51        29.46         2.73        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       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       26.99        21.60        53.16         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        30.15        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
        5.72        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-A19Q 
       34.88         4.21        13.45        28.60        42.84         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         1.71         5.62        85.74        15.72        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-A1ZR 
       30.87        12.92        12.89        47.38        52.08         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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         7.36        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.85        11.61        44.28        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.69 

  PDE1A MUTATED PDE1A WILD-TYPE 
           0.13            0.16 
  PDE1A MUTATED PDE1A WILD-TYPE 
          92.42          125.65 
  PDE1A MUTATED PDE1A WILD-TYPE 
          13.81           17.56 
[1] "0.1 - 92.4 (13.8)"  "0.2 - 125.7 (17.6)"
[1] "hr=" "1.1"
D15V2, survival
                 sevent
clus2               0   1
  PDE1A MUTATED    18  21
  PDE1A WILD-TYPE 111 120
  PDE1A MUTATED PDE1A WILD-TYPE 
             39             231 
  PDE1A MUTATED PDE1A WILD-TYPE 
             21             120 
$`PDE1A MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1IC 
       62.07       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        63.78 
TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GE 
       56.84        55.92        46.82        36.82        67.43       161.03 
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       134.40 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19F 
       71.21        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 TCGA-RP-A693 
       47.54        84.72         0.33 

$`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        86.76        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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       135.75       178.32        18.18 
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        22.29 
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        68.25        54.02        17.29        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       133.81       151.27        91.56        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        64.64         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       195.02        17.92       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.29        86.14        59.28       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32       201.80        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
      148.08        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-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05        44.05        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6.77       174.21        15.72       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        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-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26        74.73        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       39.58         6.67         0.69 

  PDE1A MUTATED PDE1A WILD-TYPE 
           0.33            0.16 
  PDE1A MUTATED PDE1A WILD-TYPE 
         208.04          357.37 
  PDE1A MUTATED PDE1A WILD-TYPE 
          55.92           50.89 
[1] "0.3 - 208.0 (55.9)" "0.2 - 357.4 (50.9)"
[1] "hr=" "1.1"
D15V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PDE1A MUTATED                    9             1
  PDE1A WILD-TYPE                 30             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PDE1A MUTATED                                           4                  25
  PDE1A WILD-TYPE                                        56                 146
D15V4, multiclass
                                           clus
vv                                          PDE1A MUTATED PDE1A WILD-TYPE
  DISTANT METASTASIS                                    9              30
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              56
  REGIONAL LYMPH NODE                                  25             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
  PDE1A MUTATED             2       0       5        1        6        3
  PDE1A WILD-TYPE           8       6      19        9       18       13
                 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        30         12         21
                 vv
clus              STAGE IIIC STAGE IV
  PDE1A MUTATED            5        3
  PDE1A WILD-TYPE         41       13
D15V5, multiclass
             clus
vv            PDE1A MUTATED PDE1A WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 0               6
  STAGE I                 5              19
  STAGE IA                1               9
  STAGE IB                6              18
  STAGE II                3              13
  STAGE IIA               2               8
  STAGE IIB               3              11
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              1              12
  STAGE IIIB              2              21
  STAGE IIIC              5              41
  STAGE IV                3              13
[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    50 47 42 54
D15V6, multiclass
       clus
vv      PDE1A MUTATED PDE1A WILD-TYPE
  T0+T1             2              50
  T2               12              47
  T3               12              42
  T4                3              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
  PDE1A MUTATED    26   6   2   2
  PDE1A WILD-TYPE 113  42  31  34
D15V7, multiclass
    clus
vv   PDE1A MUTATED PDE1A WILD-TYPE
  N0            26             113
  N1             6              42
  N2             2              31
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PDE1A MUTATED    34   2   0   0   1
  PDE1A WILD-TYPE 210   2   3   2   7
D15V8, multiclass
     clus
vv    PDE1A MUTATED PDE1A WILD-TYPE
  M0             34             210
  M1              2               2
  M1A             0               3
  M1B             0               2
  M1C             1               7
[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 86 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED     17    6
  PDE1A WILD-TYPE   86   62
     clus
vv    PDE1A MUTATED PDE1A WILD-TYPE
  NO             17              86
  YES             6              62
[1] 2 2
[1] FALSE
D15V10, binary
                 cls
clus                0   1
  PDE1A MUTATED     5  34
  PDE1A WILD-TYPE  31 205
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED      5   34
  PDE1A WILD-TYPE   31  205
     clus
vv    PDE1A MUTATED PDE1A WILD-TYPE
  NO              5              31
  YES            34             205
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, binary
                 cls
clus                0   1
  PDE1A MUTATED    13  26
  PDE1A WILD-TYPE  93 144
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED     13   26
  PDE1A WILD-TYPE   93  144
        clus
vv       PDE1A MUTATED PDE1A WILD-TYPE
  FEMALE            13              93
  MALE              26             144
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDE1A MUTATED       0                         0    39
  PDE1A WILD-TYPE     3                         1   233
D15V13, multiclass
                           clus
vv                          PDE1A MUTATED PDE1A WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                39             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"
D15V14, binary
                 cls
clus                0   1
  PDE1A MUTATED     0  39
  PDE1A WILD-TYPE   3 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE1A MUTATED      0   39
  PDE1A WILD-TYPE    3  230
                        clus
vv                       PDE1A MUTATED PDE1A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            39             230
[1] 2 2
[1] FALSE

Clustering(16) Variable = HMGCR MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  HMGCR MUTATED     3   8
  HMGCR WILD-TYPE 123 132
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             255 
  HMGCR MUTATED HMGCR WILD-TYPE 
              8             132 
$`HMGCR MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29L 
        8.52        86.76        13.32         1.12        15.85         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        44.19         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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        60.23         4.34         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        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       39.62         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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       13.45        28.60        42.84         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        23.80        14.24         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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  HMGCR MUTATED HMGCR WILD-TYPE 
           0.99            0.13 
  HMGCR MUTATED HMGCR WILD-TYPE 
          86.76          125.65 
  HMGCR MUTATED HMGCR WILD-TYPE 
          11.11           17.72 
[1] "1.0 - 86.8 (11.1)"  "0.1 - 125.7 (17.7)"
[1] "hr=" "2"  
D16V2, survival
                 sevent
clus2               0   1
  HMGCR MUTATED     3   8
  HMGCR WILD-TYPE 126 133
  HMGCR MUTATED HMGCR WILD-TYPE 
             11             259 
  HMGCR MUTATED HMGCR WILD-TYPE 
              8             133 
$`HMGCR MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29L 
       16.67        86.76        60.23        33.73        91.56         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        62.07       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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
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        63.78        72.07        64.64        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91         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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  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           53.16 
[1] "2.6 - 162.1 (33.7)" "0.2 - 357.4 (53.2)"
[1] "hr=" "2"  
D16V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  HMGCR MUTATED                    0             0
  HMGCR WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  HMGCR MUTATED                                           1                  10
  HMGCR WILD-TYPE                                        59                 161
D16V4, multiclass
                                           clus
vv                                          HMGCR MUTATED HMGCR WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                  10             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
  HMGCR MUTATED             0       0       2        0        0        1
  HMGCR WILD-TYPE          10       6      22       10       24       15
                 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        29         13         23
                 vv
clus              STAGE IIIC STAGE IV
  HMGCR MUTATED            1        0
  HMGCR WILD-TYPE         45       16
D16V5, multiclass
             clus
vv            HMGCR MUTATED HMGCR WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              22
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               3              29
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    48 59 52 55
D16V6, multiclass
       clus
vv      HMGCR MUTATED HMGCR WILD-TYPE
  T0+T1             4              48
  T2                0              59
  T3                2              52
  T4                2              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
  HMGCR MUTATED     7   1   2   1
  HMGCR WILD-TYPE 132  47  31  35
D16V7, multiclass
    clus
vv   HMGCR MUTATED HMGCR WILD-TYPE
  N0             7             132
  N1             1              47
  N2             2              31
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  HMGCR MUTATED    11   0   0   0   0
  HMGCR WILD-TYPE 233   4   3   2   8
D16V8, multiclass
     clus
vv    HMGCR MUTATED HMGCR WILD-TYPE
  M0             11             233
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 102  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      1    3
  HMGCR WILD-TYPE  102   65
     clus
vv    HMGCR MUTATED HMGCR WILD-TYPE
  NO              1             102
  YES             3              65
[1] 2 2
[1] FALSE
D16V10, binary
                 cls
clus                0   1
  HMGCR MUTATED     2   9
  HMGCR WILD-TYPE  34 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      2    9
  HMGCR WILD-TYPE   34  230
     clus
vv    HMGCR MUTATED HMGCR WILD-TYPE
  NO              2              34
  YES             9             230
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, binary
                 cls
clus                0   1
  HMGCR MUTATED     5   6
  HMGCR WILD-TYPE 101 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      5    6
  HMGCR WILD-TYPE  101  164
        clus
vv       HMGCR MUTATED HMGCR WILD-TYPE
  FEMALE             5             101
  MALE               6             164
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMGCR MUTATED       0                         0    11
  HMGCR WILD-TYPE     3                         1   261
D16V13, multiclass
                           clus
vv                          HMGCR MUTATED HMGCR WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             261
[1] 3 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   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      0   11
  HMGCR WILD-TYPE    3  258
                        clus
vv                       HMGCR MUTATED HMGCR WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             258
[1] 2 2
[1] FALSE

Clustering(17) Variable = PHGDH MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  PHGDH MUTATED     6   5
  PHGDH WILD-TYPE 120 135
  PHGDH MUTATED PHGDH WILD-TYPE 
             11             255 
  PHGDH MUTATED PHGDH WILD-TYPE 
              5             135 
$`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 TCGA-RP-A693 
       11.11         0.99        44.28        84.72         0.33 

$`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        86.76        44.19         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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55        36.85        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       11.61        31.33        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       14.70         5.79         0.69 

  PHGDH MUTATED PHGDH WILD-TYPE 
           0.33            0.13 
  PHGDH MUTATED PHGDH WILD-TYPE 
          84.72          125.65 
  PHGDH MUTATED PHGDH WILD-TYPE 
          14.56           17.33 
[1] "0.3 - 84.7 (14.6)"  "0.1 - 125.7 (17.3)"
[1] "hr=" "1.2"
D17V2, survival
                 sevent
clus2               0   1
  PHGDH MUTATED     6   5
  PHGDH WILD-TYPE 123 136
  PHGDH MUTATED PHGDH WILD-TYPE 
             11             259 
  PHGDH MUTATED PHGDH WILD-TYPE 
              5             136 
$`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 TCGA-RP-A693 
       26.37        22.92       139.89        84.72         0.33 

$`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        86.76        62.07       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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A264 
       19.30         9.90         7.23         2.04        11.74       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 
TCGA-RP-A694 
        0.69 

  PHGDH MUTATED PHGDH WILD-TYPE 
           0.33            0.16 
  PHGDH MUTATED PHGDH WILD-TYPE 
         204.66          357.37 
  PHGDH MUTATED PHGDH WILD-TYPE 
          48.72           52.01 
[1] "0.3 - 204.7 (48.7)" "0.2 - 357.4 (52.0)"
[1] "hr=" "1.1"
D17V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PHGDH MUTATED                    1             0
  PHGDH WILD-TYPE                 38             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PHGDH MUTATED                                           2                   8
  PHGDH WILD-TYPE                                        58                 163
D17V4, multiclass
                                           clus
vv                                          PHGDH MUTATED PHGDH WILD-TYPE
  DISTANT METASTASIS                                    1              38
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   8             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
  PHGDH MUTATED             0       0       1        1        0        0
  PHGDH WILD-TYPE          10       6      23        9       24       16
                 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        30         13         23
                 vv
clus              STAGE IIIC STAGE IV
  PHGDH MUTATED            2        1
  PHGDH WILD-TYPE         44       15
D17V5, multiclass
             clus
vv            PHGDH MUTATED PHGDH WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                1               9
  STAGE IB                0              24
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              2              44
  STAGE IV                1              15
[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    50 59 54 53
D17V6, multiclass
       clus
vv      PHGDH MUTATED PHGDH WILD-TYPE
  T0+T1             2              50
  T2                0              59
  T3                0              54
  T4                4              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
  PHGDH MUTATED     4   2   1   1
  PHGDH WILD-TYPE 135  46  32  35
D17V7, multiclass
    clus
vv   PHGDH MUTATED PHGDH WILD-TYPE
  N0             4             135
  N1             2              46
  N2             1              32
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PHGDH MUTATED     8   0   0   0   1
  PHGDH WILD-TYPE 236   4   3   2   7
D17V8, multiclass
     clus
vv    PHGDH MUTATED PHGDH WILD-TYPE
  M0              8             236
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             1               7
[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 102  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      1    2
  PHGDH WILD-TYPE  102   66
     clus
vv    PHGDH MUTATED PHGDH WILD-TYPE
  NO              1             102
  YES             2              66
[1] 2 2
[1] FALSE
D17V10, binary
                 cls
clus                0   1
  PHGDH MUTATED     2   9
  PHGDH WILD-TYPE  34 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      2    9
  PHGDH WILD-TYPE   34  230
     clus
vv    PHGDH MUTATED PHGDH WILD-TYPE
  NO              2              34
  YES             9             230
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, binary
                 cls
clus                0   1
  PHGDH MUTATED     2   9
  PHGDH WILD-TYPE 104 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      2    9
  PHGDH WILD-TYPE  104  161
        clus
vv       PHGDH MUTATED PHGDH WILD-TYPE
  FEMALE             2             104
  MALE               9             161
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHGDH MUTATED       0                         0    11
  PHGDH WILD-TYPE     3                         1   261
D17V13, multiclass
                           clus
vv                          PHGDH MUTATED PHGDH WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             261
[1] 3 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  11
  PHGDH WILD-TYPE   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHGDH MUTATED      0   11
  PHGDH WILD-TYPE    3  258
                        clus
vv                       PHGDH MUTATED PHGDH WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             258
[1] 2 2
[1] FALSE

Clustering(18) Variable = SLC38A4 MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  SLC38A4 MUTATED    18  15
  SLC38A4 WILD-TYPE 108 125
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               33               233 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               15               125 
$`SLC38A4 MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A51T TCGA-D3-A5GO TCGA-DA-A1I1 
       11.41        44.19         6.31        25.78        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        39.62        11.31        36.30        30.08        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       63.42        53.16        52.67        21.60        22.22        27.35 
TCGA-ER-A19A TCGA-ER-A19G TCGA-FW-A3R5 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 
       76.41       114.15         0.99         7.23        11.61        84.72 
TCGA-GN-A266 TCGA-QB-A6FS TCGA-RP-A693 
       10.13         5.79         0.33 

$`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        86.76         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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       32.61        52.01        13.68        17.72        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       21.93         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-A5UL TCGA-EB-A5UN 
       14.83         0.20        23.15        19.00        13.35        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-A20F TCGA-EE-A20I TCGA-EE-A29B 
        5.13         4.31        60.23        15.85         1.18         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       37.97        11.15        62.79        36.85         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
        8.09        49.22         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       60.49         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14         0.95        18.41        21.73        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-A19H TCGA-ER-A19J 
        3.78         3.52        11.90        11.11        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16        17.33         9.90         0.85        44.28        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A694 
       16.24        15.42        12.16        14.70         0.69 

  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
             0.33              0.13 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           114.15            125.65 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
            14.56             17.33 
[1] "0.3 - 114.2 (14.6)" "0.1 - 125.7 (17.3)"
[1] "hr=" "1.2"
D18V2, survival
                   sevent
clus2                 0   1
  SLC38A4 MUTATED    19  15
  SLC38A4 WILD-TYPE 110 126
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               34               236 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               15               126 
$`SLC38A4 MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A1JW 
       11.87        62.07        12.10        26.89       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        56.84        46.82        36.82        48.72 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JA 
      204.66        96.23       162.48        71.21        36.95        53.19 
TCGA-EE-A3JD TCGA-ER-A19A TCGA-ER-A19G TCGA-FW-A3R5 TCGA-GF-A4EO TCGA-GF-A6C9 
       27.35        77.75       268.93        22.92         7.23        11.74 
TCGA-GN-A265 TCGA-GN-A266 TCGA-QB-A6FS TCGA-RP-A693 
       84.72        10.13         6.67         0.33 

$`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        86.76       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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       63.81       135.75       178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       91.56        13.55        80.61        47.84        13.97        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         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       195.02        17.92       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73       103.20        16.96       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23       134.40        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB 
      138.81       172.18       127.20        64.08        34.32       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       50.76         9.17        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        2.04       139.89       117.93        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-RP-A694 
       39.58         0.69 

  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
             0.33              0.16 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           268.93            357.37 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           50.955            51.815 
[1] "0.3 - 268.9 (51.0)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.2"
D18V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC38A4 MUTATED                    7             0
  SLC38A4 WILD-TYPE                 32             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC38A4 MUTATED                                           6
  SLC38A4 WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  SLC38A4 MUTATED                    21
  SLC38A4 WILD-TYPE                 150
D18V4, multiclass
                                           clus
vv                                          SLC38A4 MUTATED SLC38A4 WILD-TYPE
  DISTANT METASTASIS                                      7                32
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                54
  REGIONAL LYMPH NODE                                    21               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
  SLC38A4 MUTATED             0       1       1        2        3        3
  SLC38A4 WILD-TYPE          10       5      23        8       21       13
                   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        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC38A4 MUTATED            2          8        2
  SLC38A4 WILD-TYPE         21         38       14
D18V5, multiclass
             clus
vv            SLC38A4 MUTATED SLC38A4 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   1                23
  STAGE IA                  2                 8
  STAGE IB                  3                21
  STAGE II                  3                13
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 0                 9
  STAGE III                 4                28
  STAGE IIIA                2                11
  STAGE IIIB                2                21
  STAGE IIIC                8                38
  STAGE IV                  2                14
[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       6  4  5  9
  SLC38A4 WILD-TYPE    46 55 49 48
D18V6, multiclass
       clus
vv      SLC38A4 MUTATED SLC38A4 WILD-TYPE
  T0+T1               6                46
  T2                  4                55
  T3                  5                49
  T4                  9                48
[1] 4 2
[1] TRUE
[1] "dimension of 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   4
  SLC38A4 WILD-TYPE 124  43  27  32
D18V7, multiclass
    clus
vv   SLC38A4 MUTATED SLC38A4 WILD-TYPE
  N0              15               124
  N1               5                43
  N2               6                27
  N3               4                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
  SLC38A4 MUTATED    29   1   0   0   1
  SLC38A4 WILD-TYPE 215   3   3   2   7
D18V8, multiclass
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  M0               29               215
  M1                1                 3
  M1A               0                 3
  M1B               0                 2
  M1C               1                 7
[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 89 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED     14    5
  SLC38A4 WILD-TYPE   89   63
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  NO               14                89
  YES               5                63
[1] 2 2
[1] FALSE
D18V10, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     9  25
  SLC38A4 WILD-TYPE  27 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      9   25
  SLC38A4 WILD-TYPE   27  214
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  NO                9                27
  YES              25               214
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     7  27
  SLC38A4 WILD-TYPE  99 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      7   27
  SLC38A4 WILD-TYPE   99  143
        clus
vv       SLC38A4 MUTATED SLC38A4 WILD-TYPE
  FEMALE               7                99
  MALE                27               143
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC38A4 MUTATED       1                         0    33
  SLC38A4 WILD-TYPE     2                         1   239
D18V13, multiclass
                           clus
vv                          SLC38A4 MUTATED SLC38A4 WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  33               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"
D18V14, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     0  33
  SLC38A4 WILD-TYPE   3 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      0   33
  SLC38A4 WILD-TYPE    3  236
                        clus
vv                       SLC38A4 MUTATED SLC38A4 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              33               236
[1] 2 2
[1] FALSE

Clustering(19) Variable = CDK4 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  CDK4 MUTATED     1   6
  CDK4 WILD-TYPE 125 134
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            259 
  CDK4 MUTATED CDK4 WILD-TYPE 
             6            134 
$`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 
        0.85 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL 
       17.56        14.83        13.15        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69 
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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73         7.96        14.56        63.42       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       52.67         5.56       124.31       122.73        51.62        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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19F 
        5.72        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-A19T TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  CDK4 MUTATED CDK4 WILD-TYPE 
          0.20           0.13 
  CDK4 MUTATED CDK4 WILD-TYPE 
         44.25         125.65 
  CDK4 MUTATED CDK4 WILD-TYPE 
          3.68          17.56 
[1] "0.2 - 44.2 (3.7)"   "0.1 - 125.7 (17.6)"
[1] "hr=" "3.4"
D19V2, survival
                sevent
clus2              0   1
  CDK4 MUTATED     1   6
  CDK4 WILD-TYPE 128 135
  CDK4 MUTATED CDK4 WILD-TYPE 
             7            263 
  CDK4 MUTATED CDK4 WILD-TYPE 
             6            135 
$`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 
        2.04 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        51.62        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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        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-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-A6C9 
       47.54         0.16        19.30         9.90         7.23        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  CDK4 MUTATED CDK4 WILD-TYPE 
          2.04           0.16 
  CDK4 MUTATED CDK4 WILD-TYPE 
        148.18         357.37 
  CDK4 MUTATED CDK4 WILD-TYPE 
         13.02          53.16 
[1] "2.0 - 148.2 (13.0)" "0.2 - 357.4 (53.2)"
[1] "hr=" "3.1"
D19V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  CDK4 MUTATED                    1             0
  CDK4 WILD-TYPE                 38             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CDK4 MUTATED                                           1                   5
  CDK4 WILD-TYPE                                        59                 166
D19V4, multiclass
                                           clus
vv                                          CDK4 MUTATED CDK4 WILD-TYPE
  DISTANT METASTASIS                                   1             38
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            1             59
  REGIONAL LYMPH NODE                                  5            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
  CDK4 MUTATED             0       0       1        0        1        0
  CDK4 WILD-TYPE          10       6      23       10       23       16
                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        31         13         22
                vv
clus             STAGE IIIC STAGE IV
  CDK4 MUTATED            1        0
  CDK4 WILD-TYPE         45       16
D19V5, multiclass
             clus
vv            CDK4 MUTATED CDK4 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             23
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             16
  STAGE IIA              0             10
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              1             31
  STAGE IIIA             0             13
  STAGE IIIB             1             22
  STAGE IIIC             1             45
  STAGE IV               0             16
[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    51 57 52 57
D19V6, multiclass
       clus
vv      CDK4 MUTATED CDK4 WILD-TYPE
  T0+T1            1             51
  T2               2             57
  T3               2             52
  T4               0             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CDK4 MUTATED     2   2   1   0
  CDK4 WILD-TYPE 137  46  32  36
D19V7, multiclass
    clus
vv   CDK4 MUTATED CDK4 WILD-TYPE
  N0            2            137
  N1            2             46
  N2            1             32
  N3            0             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              M0  M1 M1A M1B M1C
  CDK4 MUTATED     6   0   0   0   0
  CDK4 WILD-TYPE 238   4   3   2   8
D19V8, multiclass
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  M0             6            238
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 101  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      2    2
  CDK4 WILD-TYPE  101   66
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  NO             2            101
  YES            2             66
[1] 2 2
[1] FALSE
D19V10, binary
                cls
clus               0   1
  CDK4 MUTATED     1   6
  CDK4 WILD-TYPE  35 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      1    6
  CDK4 WILD-TYPE   35  233
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  NO             1             35
  YES            6            233
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, binary
                cls
clus               0   1
  CDK4 MUTATED     3   4
  CDK4 WILD-TYPE 103 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      3    4
  CDK4 WILD-TYPE  103  166
        clus
vv       CDK4 MUTATED CDK4 WILD-TYPE
  FEMALE            3            103
  MALE              4            166
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDK4 MUTATED       1                         0     6
  CDK4 WILD-TYPE     2                         1   266
D19V13, multiclass
                           clus
vv                          CDK4 MUTATED CDK4 WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                6            266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                cls
clus               0   1
  CDK4 MUTATED     0   7
  CDK4 WILD-TYPE   3 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      0    7
  CDK4 WILD-TYPE    3  262
                        clus
vv                       CDK4 MUTATED CDK4 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            7            262
[1] 2 2
[1] FALSE

Clustering(20) Variable = FAM58A MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  FAM58A MUTATED     1   4
  FAM58A WILD-TYPE 125 136
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              261 
  FAM58A MUTATED FAM58A WILD-TYPE 
               4              136 
$`FAM58A MUTATED`
TCGA-DA-A1IC TCGA-EE-A29N TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD 
        6.64         9.50        52.67        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  FAM58A MUTATED FAM58A WILD-TYPE 
            6.64             0.13 
  FAM58A MUTATED FAM58A WILD-TYPE 
           52.67           125.65 
  FAM58A MUTATED FAM58A WILD-TYPE 
           21.60            16.47 
[1] "6.6 - 52.7 (21.6)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.6"
D20V2, survival
                  sevent
clus2                0   1
  FAM58A MUTATED     1   4
  FAM58A WILD-TYPE 128 137
  FAM58A MUTATED FAM58A WILD-TYPE 
               5              265 
  FAM58A MUTATED FAM58A WILD-TYPE 
               4              137 
$`FAM58A MUTATED`
TCGA-DA-A1IC TCGA-EE-A29N TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD 
       68.09        18.61        71.21        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       47.54       248.65        43.23       134.40       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19       201.80        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  FAM58A MUTATED FAM58A WILD-TYPE 
           18.61             0.16 
  FAM58A MUTATED FAM58A WILD-TYPE 
           71.21           357.37 
  FAM58A MUTATED FAM58A WILD-TYPE 
           36.95            52.01 
[1] "18.6 - 71.2 (37.0)" "0.2 - 357.4 (52.0)"
[1] "hr=" "2.2"
D20V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  FAM58A MUTATED                    0             0
  FAM58A WILD-TYPE                 39             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  FAM58A MUTATED                                           2
  FAM58A WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  FAM58A MUTATED                     3
  FAM58A WILD-TYPE                 168
D20V4, multiclass
                                           clus
vv                                          FAM58A MUTATED FAM58A WILD-TYPE
  DISTANT METASTASIS                                     0               39
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                    3              168
[1] 4 2
[1] 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      24       10       23       16
                  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        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  FAM58A MUTATED            1          0        0
  FAM58A WILD-TYPE         22         46       16
D20V5, multiclass
             clus
vv            FAM58A MUTATED FAM58A WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  0               24
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 0               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               0               13
  STAGE IIIB               1               22
  STAGE IIIC               0               46
  STAGE IV                 0               16
[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    52 58 53 56
D20V6, multiclass
       clus
vv      FAM58A MUTATED FAM58A WILD-TYPE
  T0+T1              0               52
  T2                 1               58
  T3                 1               53
  T4                 1               56
[1] 4 2
[1] TRUE
[1] "dimension of 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 137  47  31  36
D20V7, multiclass
    clus
vv   FAM58A MUTATED FAM58A WILD-TYPE
  N0              2              137
  N1              1               47
  N2              2               31
  N3              0               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                M0  M1 M1A M1B M1C
  FAM58A MUTATED     5   0   0   0   0
  FAM58A WILD-TYPE 239   4   3   2   8
D20V8, multiclass
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  M0               5              239
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 100  68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      3    0
  FAM58A WILD-TYPE  100   68
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  NO               3              100
  YES              0               68
[1] 2 2
[1] FALSE
D20V10, binary
                  cls
clus                 0   1
  FAM58A MUTATED     1   4
  FAM58A WILD-TYPE  35 235
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      1    4
  FAM58A WILD-TYPE   35  235
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  NO               1               35
  YES              4              235
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, binary
                  cls
clus                 0   1
  FAM58A MUTATED     0   5
  FAM58A WILD-TYPE 106 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      0    5
  FAM58A WILD-TYPE  106  165
        clus
vv       FAM58A MUTATED FAM58A WILD-TYPE
  FEMALE              0              106
  MALE                5              165
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM58A MUTATED       0                         0     5
  FAM58A WILD-TYPE     3                         1   267
D20V13, multiclass
                           clus
vv                          FAM58A MUTATED FAM58A WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  5              267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                  cls
clus                 0   1
  FAM58A MUTATED     0   5
  FAM58A WILD-TYPE   3 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      0    5
  FAM58A WILD-TYPE    3  264
                        clus
vv                       FAM58A MUTATED FAM58A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5              264
[1] 2 2
[1] FALSE

Clustering(21) Variable = EMG1 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     3   5
  EMG1 WILD-TYPE 123 135
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            258 
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            135 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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-A20F TCGA-EE-A20H 
       12.20         5.13         4.31        60.23        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        22.22         0.95        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       19.53         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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  EMG1 MUTATED EMG1 WILD-TYPE 
          2.27           0.13 
  EMG1 MUTATED EMG1 WILD-TYPE 
         82.29         125.65 
  EMG1 MUTATED EMG1 WILD-TYPE 
          7.71          17.72 
[1] "2.3 - 82.3 (7.7)"   "0.1 - 125.7 (17.7)"
[1] "hr=" "2"  
D21V2, survival
                sevent
clus2              0   1
  EMG1 MUTATED     3   5
  EMG1 WILD-TYPE 126 136
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            262 
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            136 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JA 
      138.81       172.18       127.20        36.95        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       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-A19J 
       48.89        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-A1ZG 
       27.72        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-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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  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         51.815 
[1] "12.6 - 166.5 (50.3)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1.3"
D21V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  EMG1 MUTATED                    3             1
  EMG1 WILD-TYPE                 36             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  EMG1 MUTATED                                           2                   2
  EMG1 WILD-TYPE                                        58                 169
D21V4, multiclass
                                           clus
vv                                          EMG1 MUTATED EMG1 WILD-TYPE
  DISTANT METASTASIS                                   3             36
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            2             58
  REGIONAL LYMPH NODE                                  2            169
[1] 4 2
[1] 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      24       10       23       16
                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        32         11         23
                vv
clus             STAGE IIIC STAGE IV
  EMG1 MUTATED            2        0
  EMG1 WILD-TYPE         44       16
D21V5, multiclass
             clus
vv            EMG1 MUTATED EMG1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                0             24
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             16
  STAGE IIA              0             10
  STAGE IIB              0             14
  STAGE IIC              1              8
  STAGE III              0             32
  STAGE IIIA             2             11
  STAGE IIIB             0             23
  STAGE IIIC             2             44
  STAGE IV               0             16
[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    52 56 52 55
D21V6, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  T0+T1            0             52
  T2               3             56
  T3               2             52
  T4               2             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
  EMG1 MUTATED     4   3   0   1
  EMG1 WILD-TYPE 135  45  33  35
D21V7, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  N0            4            135
  N1            3             45
  N2            0             33
  N3            1             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  EMG1 MUTATED     8   0   0   0   0
  EMG1 WILD-TYPE 236   4   3   2   8
D21V8, multiclass
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  M0             8            236
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 100  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      3    2
  EMG1 WILD-TYPE  100   66
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             3            100
  YES            2             66
[1] 2 2
[1] FALSE
D21V10, binary
                cls
clus               0   1
  EMG1 MUTATED     0   8
  EMG1 WILD-TYPE  36 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    8
  EMG1 WILD-TYPE   36  231
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             0             36
  YES            8            231
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, binary
                cls
clus               0   1
  EMG1 MUTATED     3   5
  EMG1 WILD-TYPE 103 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      3    5
  EMG1 WILD-TYPE  103  165
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            3            103
  MALE              5            165
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED       0                         0     8
  EMG1 WILD-TYPE     3                         1   264
D21V13, multiclass
                           clus
vv                          EMG1 MUTATED EMG1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                8            264
[1] 3 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   3 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    8
  EMG1 WILD-TYPE    3  261
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            8            261
[1] 2 2
[1] FALSE

Clustering(22) Variable = RQCD1 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  RQCD1 MUTATED     5   3
  RQCD1 WILD-TYPE 121 137
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              8             258 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              3             137 
$`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 TCGA-RP-A694 
        8.68         0.69 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50         8.09         8.84         9.99         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A44A 
        9.04         6.58        22.49         1.71         5.62        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 

  RQCD1 MUTATED RQCD1 WILD-TYPE 
           0.69            0.13 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
          34.68          125.65 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
         13.120          17.445 
[1] "0.7 - 34.7 (13.1)"  "0.1 - 125.7 (17.4)"
[1] "hr=" "1.1"
D22V2, survival
                 sevent
clus2               0   1
  RQCD1 MUTATED     5   3
  RQCD1 WILD-TYPE 124 138
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              8             262 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              3             138 
$`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 TCGA-RP-A694 
       26.56         0.69 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       72.07        64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21         6.77       174.21        15.72       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-A1ZW TCGA-FS-A1ZY 
      133.55        11.41       148.80        53.16        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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       32.48        39.58         6.67         0.33 

  RQCD1 MUTATED RQCD1 WILD-TYPE 
           0.69            0.16 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
         162.08          357.37 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
         61.335          51.120 
[1] "0.7 - 162.1 (61.3)" "0.2 - 357.4 (51.1)"
[1] "hr=" "1.3"
D22V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  RQCD1 MUTATED                    2             1
  RQCD1 WILD-TYPE                 37             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RQCD1 MUTATED                                           3                   3
  RQCD1 WILD-TYPE                                        57                 168
D22V4, multiclass
                                           clus
vv                                          RQCD1 MUTATED RQCD1 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             3              57
  REGIONAL LYMPH NODE                                   3             168
[1] 4 2
[1] 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      24       10       22       16
                 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        32         12         23
                 vv
clus              STAGE IIIC STAGE IV
  RQCD1 MUTATED            0        1
  RQCD1 WILD-TYPE         46       15
D22V5, multiclass
             clus
vv            RQCD1 MUTATED RQCD1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               3               6
  STAGE III               0              32
  STAGE IIIA              1              12
  STAGE IIIB              0              23
  STAGE IIIC              0              46
  STAGE IV                1              15
[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    52 57 53 54
D22V6, multiclass
       clus
vv      RQCD1 MUTATED RQCD1 WILD-TYPE
  T0+T1             0              52
  T2                2              57
  T3                1              53
  T4                3              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
  RQCD1 MUTATED     7   1   0   0
  RQCD1 WILD-TYPE 132  47  33  36
D22V7, multiclass
    clus
vv   RQCD1 MUTATED RQCD1 WILD-TYPE
  N0             7             132
  N1             1              47
  N2             0              33
  N3             0              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               M0  M1 M1A M1B M1C
  RQCD1 MUTATED     8   0   0   0   1
  RQCD1 WILD-TYPE 236   4   3   2   7
D22V8, multiclass
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  M0              8             236
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             1               7
[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 100  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      3    3
  RQCD1 WILD-TYPE  100   65
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  NO              3             100
  YES             3              65
[1] 2 2
[1] FALSE
D22V10, binary
                 cls
clus                0   1
  RQCD1 MUTATED     1   8
  RQCD1 WILD-TYPE  35 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      1    8
  RQCD1 WILD-TYPE   35  231
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  NO              1              35
  YES             8             231
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, binary
                 cls
clus                0   1
  RQCD1 MUTATED     6   3
  RQCD1 WILD-TYPE 100 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      6    3
  RQCD1 WILD-TYPE  100  167
        clus
vv       RQCD1 MUTATED RQCD1 WILD-TYPE
  FEMALE             6             100
  MALE               3             167
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RQCD1 MUTATED       0                         0     9
  RQCD1 WILD-TYPE     3                         1   263
D22V13, multiclass
                           clus
vv                          RQCD1 MUTATED RQCD1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                 cls
clus                0   1
  RQCD1 MUTATED     0   9
  RQCD1 WILD-TYPE   3 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      0    9
  RQCD1 WILD-TYPE    3  260
                        clus
vv                       RQCD1 MUTATED RQCD1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             260
[1] 2 2
[1] FALSE

Clustering(23) Variable = HSD11B1 MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2                 0   1
  HSD11B1 MUTATED    10   4
  HSD11B1 WILD-TYPE 116 136
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               252 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                4               136 
$`HSD11B1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A51T TCGA-EB-A5SG TCGA-EE-A29M 
       70.16        44.19        36.16        25.78        23.15        39.62 
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        60.49 
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        86.76        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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.61        52.01        47.87        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        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 
       60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
        1.08         9.50        12.03         8.09         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       32.15         8.09        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        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       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        26.99        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       16.24        15.42        12.16        14.70         0.33         0.69 

  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
             0.99              0.13 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
            70.16            125.65 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           24.465            16.190 
[1] "1.0 - 70.2 (24.5)"  "0.1 - 125.7 (16.2)"
[1] "hr=" "2.1"
D23V2, survival
                   sevent
clus2                 0   1
  HSD11B1 MUTATED    10   4
  HSD11B1 WILD-TYPE 119 137
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               256 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                4               137 
$`HSD11B1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A51T TCGA-EB-A5SG TCGA-EE-A29M 
       71.80        62.07        42.08        26.89        68.25        56.84 
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       134.40 
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        86.76        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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81       135.75       137.92       178.32        18.18       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        22.29 
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        54.02        17.29 
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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        63.78        72.07        64.64         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       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       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       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         0.33         0.69 

  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
             6.67              0.16 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           134.40            357.37 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           47.050            52.585 
[1] "6.7 - 134.4 (47.0)" "0.2 - 357.4 (52.6)"
[1] "hr=" "1.4"
D23V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  HSD11B1 MUTATED                    1             0
  HSD11B1 WILD-TYPE                 38             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  HSD11B1 MUTATED                                           3
  HSD11B1 WILD-TYPE                                        57
                   vv
clus                REGIONAL LYMPH NODE
  HSD11B1 MUTATED                    10
  HSD11B1 WILD-TYPE                 161
D23V4, multiclass
                                           clus
vv                                          HSD11B1 MUTATED HSD11B1 WILD-TYPE
  DISTANT METASTASIS                                      1                38
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                57
  REGIONAL LYMPH NODE                                    10               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
  HSD11B1 MUTATED             0       0       1        1        2        1
  HSD11B1 WILD-TYPE          10       6      23        9       22       15
                   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        30         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  HSD11B1 MUTATED            0          3        0
  HSD11B1 WILD-TYPE         23         43       16
D23V5, multiclass
             clus
vv            HSD11B1 MUTATED HSD11B1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   1                23
  STAGE IA                  1                 9
  STAGE IB                  2                22
  STAGE II                  1                15
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 1                 8
  STAGE III                 2                30
  STAGE IIIA                1                12
  STAGE IIIB                0                23
  STAGE IIIC                3                43
  STAGE IV                  0                16
[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    49 57 50 54
D23V6, multiclass
       clus
vv      HSD11B1 MUTATED HSD11B1 WILD-TYPE
  T0+T1               3                49
  T2                  2                57
  T3                  4                50
  T4                  3                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
  HSD11B1 MUTATED     7   3   2   1
  HSD11B1 WILD-TYPE 132  45  31  35
D23V7, multiclass
    clus
vv   HSD11B1 MUTATED HSD11B1 WILD-TYPE
  N0               7               132
  N1               3                45
  N2               2                31
  N3               1                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  HSD11B1 MUTATED    13   0   0   0   0
  HSD11B1 WILD-TYPE 231   4   3   2   8
D23V8, multiclass
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  M0               13               231
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 96 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      7    4
  HSD11B1 WILD-TYPE   96   64
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO                7                96
  YES               4                64
[1] 2 2
[1] FALSE
D23V10, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     1  13
  HSD11B1 WILD-TYPE  35 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      1   13
  HSD11B1 WILD-TYPE   35  226
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO                1                35
  YES              13               226
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     7   7
  HSD11B1 WILD-TYPE  99 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      7    7
  HSD11B1 WILD-TYPE   99  163
        clus
vv       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  FEMALE               7                99
  MALE                 7               163
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSD11B1 MUTATED       0                         0    14
  HSD11B1 WILD-TYPE     3                         1   258
D23V13, multiclass
                           clus
vv                          HSD11B1 MUTATED HSD11B1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  14               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"
D23V14, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     0  14
  HSD11B1 WILD-TYPE   3 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      0   14
  HSD11B1 WILD-TYPE    3  255
                        clus
vv                       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              14               255
[1] 2 2
[1] FALSE

Clustering(24) Variable = DMC1 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  DMC1 MUTATED     7   5
  DMC1 WILD-TYPE 119 135
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            254 
  DMC1 MUTATED DMC1 WILD-TYPE 
             5            135 
$`DMC1 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-EB-A5SG TCGA-EE-A29A TCGA-EE-A29G 
        8.52        29.23        36.69        23.15         7.99         8.55 
TCGA-EE-A29S TCGA-EE-A2MR TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19M TCGA-GF-A3OT 
        9.99        60.49        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        86.76        11.41        44.19 
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 
       59.57       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        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20        19.00        13.35        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        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        11.15        62.79        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       39.62         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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       11.11       114.15        34.88         4.21        13.45        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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        17.33 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  DMC1 MUTATED DMC1 WILD-TYPE 
          7.99           0.13 
  DMC1 MUTATED DMC1 WILD-TYPE 
         76.41         125.65 
  DMC1 MUTATED DMC1 WILD-TYPE 
        22.375         16.355 
[1] "8.0 - 76.4 (22.4)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1.3"
D24V2, survival
                sevent
clus2              0   1
  DMC1 MUTATED     7   5
  DMC1 WILD-TYPE 122 136
  DMC1 MUTATED DMC1 WILD-TYPE 
            12            258 
  DMC1 MUTATED DMC1 WILD-TYPE 
             5            136 
$`DMC1 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-EB-A5SG TCGA-EE-A29A TCGA-EE-A29G 
       16.67        45.30        61.18        68.25        63.35        72.07 
TCGA-EE-A29S TCGA-EE-A2MR TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19M TCGA-GF-A3OT 
       55.92       134.40        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        86.76        11.87        62.07 
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 
       59.57       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       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56       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        63.78        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       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       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-A4EO TCGA-GF-A6C8 
       22.92        47.54         0.16        19.30         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  DMC1 MUTATED DMC1 WILD-TYPE 
          9.90           0.16 
  DMC1 MUTATED DMC1 WILD-TYPE 
        134.40         357.37 
  DMC1 MUTATED DMC1 WILD-TYPE 
        62.265         50.825 
[1] "9.9 - 134.4 (62.3)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1.1"
D24V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  DMC1 MUTATED                    1             0
  DMC1 WILD-TYPE                 38             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DMC1 MUTATED                                           5                   6
  DMC1 WILD-TYPE                                        55                 165
D24V4, multiclass
                                           clus
vv                                          DMC1 MUTATED DMC1 WILD-TYPE
  DISTANT METASTASIS                                   1             38
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            5             55
  REGIONAL LYMPH NODE                                  6            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
  DMC1 MUTATED             0       0       2        0        1        0
  DMC1 WILD-TYPE          10       6      22       10       23       16
                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        32         11         21
                vv
clus             STAGE IIIC STAGE IV
  DMC1 MUTATED            1        1
  DMC1 WILD-TYPE         45       15
D24V5, multiclass
             clus
vv            DMC1 MUTATED DMC1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                2             22
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             16
  STAGE IIA              1              9
  STAGE IIB              0             14
  STAGE IIC              1              8
  STAGE III              0             32
  STAGE IIIA             2             11
  STAGE IIIB             2             21
  STAGE IIIC             1             45
  STAGE IV               1             15
[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    51 55 51 55
D24V6, multiclass
       clus
vv      DMC1 MUTATED DMC1 WILD-TYPE
  T0+T1            1             51
  T2               4             55
  T3               3             51
  T4               2             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
  DMC1 MUTATED     6   1   3   1
  DMC1 WILD-TYPE 133  47  30  35
D24V7, multiclass
    clus
vv   DMC1 MUTATED DMC1 WILD-TYPE
  N0            6            133
  N1            1             47
  N2            3             30
  N3            1             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  DMC1 MUTATED    10   1   0   0   0
  DMC1 WILD-TYPE 234   3   3   2   8
D24V8, multiclass
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  M0            10            234
  M1             1              3
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 97 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      6    3
  DMC1 WILD-TYPE   97   65
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO             6             97
  YES            3             65
[1] 2 2
[1] FALSE
D24V10, binary
                cls
clus               0   1
  DMC1 MUTATED     2  10
  DMC1 WILD-TYPE  34 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      2   10
  DMC1 WILD-TYPE   34  229
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO             2             34
  YES           10            229
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, binary
                cls
clus               0   1
  DMC1 MUTATED     3   9
  DMC1 WILD-TYPE 103 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      3    9
  DMC1 WILD-TYPE  103  161
        clus
vv       DMC1 MUTATED DMC1 WILD-TYPE
  FEMALE            3            103
  MALE              9            161
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DMC1 MUTATED       0                         0    12
  DMC1 WILD-TYPE     3                         1   260
D24V13, multiclass
                           clus
vv                          DMC1 MUTATED DMC1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               12            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"
D24V14, binary
                cls
clus               0   1
  DMC1 MUTATED     0  11
  DMC1 WILD-TYPE   3 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      0   11
  DMC1 WILD-TYPE    3  258
                        clus
vv                       DMC1 MUTATED DMC1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           11            258
[1] 2 2
[1] FALSE

Clustering(25) Variable = NRK MUTATION ANALYSIS
D25V1, survival
               sevent
clus2             0   1
  NRK MUTATED    24  18
  NRK WILD-TYPE 102 122
  NRK MUTATED NRK WILD-TYPE 
           42           224 
  NRK MUTATED NRK WILD-TYPE 
           18           122 
$`NRK MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU 
        8.38        44.19        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        13.68        13.22        36.69         6.64 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       13.35        13.22         6.31        12.20         4.31        15.85 
TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD 
        8.09        49.22         9.67         1.15        13.02         9.53 
TCGA-EE-A2MQ TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19S 
       21.60        13.81        22.92        21.60        27.35        36.07 
TCGA-ER-A1A1 TCGA-ER-A42K TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A4F0 
       78.44         5.62        11.01        20.38        12.89        53.85 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 
        6.41         0.99         0.13        17.33         9.90        11.61 

$`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        86.76        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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GS 
       54.31        32.28        21.44        32.61        25.78        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01        21.93         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        23.15        19.00 
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 
       60.23         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        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       39.62         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 
       32.15         8.09        11.31        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        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       125.65       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 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        30.15        15.95        12.72         3.22 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
       34.68         9.57         6.58        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        15.72        64.47 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        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-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-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-A4FD TCGA-FW-A3I3 
       28.73        14.20        10.78         5.98         2.27         0.20 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.16         7.23         0.85        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  NRK MUTATED NRK WILD-TYPE 
         0.13          0.16 
  NRK MUTATED NRK WILD-TYPE 
       103.59        125.65 
  NRK MUTATED NRK WILD-TYPE 
       13.515        17.850 
[1] "0.1 - 103.6 (13.5)" "0.2 - 125.7 (17.9)"
[1] "hr=" "1.2"
D25V2, survival
               sevent
clus2             0   1
  NRK MUTATED    24  18
  NRK WILD-TYPE 105 123
  NRK MUTATED NRK WILD-TYPE 
           42           228 
  NRK MUTATED NRK WILD-TYPE 
           18           123 
$`NRK MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU 
       65.49        62.07        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       178.32        66.25        61.18        68.09 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       17.29        52.01         8.65        26.89         4.96        91.56 
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-ER-A42K TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A4F0 
       79.99         6.77       228.59       357.37        23.93        77.82 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 
       49.45        22.92        47.54        19.30         9.90        11.74 

$`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        86.76        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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GS 
      145.12        32.94        22.62        63.81        26.89        18.18 
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 
       22.29         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        68.25        54.02        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       133.81       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 
       63.78        72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       46.82        36.82        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51        23.47       138.81       172.18        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19       201.80        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       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-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       92.98       174.21        15.72       216.92        48.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
       20.91        28.08         7.79        27.72        48.85        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-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-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A4EO 
       12.43        26.73        77.88         0.20         0.16         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  NRK MUTATED NRK WILD-TYPE 
         4.96          0.16 
  NRK MUTATED NRK WILD-TYPE 
       357.37        314.56 
  NRK MUTATED NRK WILD-TYPE 
       47.410        53.225 
[1] "5.0 - 357.4 (47.4)" "0.2 - 314.6 (53.2)"
[1] "hr=" "1.3"
D25V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NRK MUTATED                    9             1
  NRK WILD-TYPE                 30             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NRK MUTATED                                          12                  21
  NRK WILD-TYPE                                        48                 150
D25V4, multiclass
                                           clus
vv                                          NRK MUTATED NRK WILD-TYPE
  DISTANT METASTASIS                                  9            30
  PRIMARY TUMOR                                       1             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE          12            48
  REGIONAL LYMPH NODE                                21           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
  NRK MUTATED             2       1       2        1        4        5
  NRK WILD-TYPE           8       5      22        9       20       11
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NRK MUTATED           2         3         1         8          3          3
  NRK WILD-TYPE         8        11         8        24         10         20
               vv
clus            STAGE IIIC STAGE IV
  NRK MUTATED            6        0
  NRK WILD-TYPE         40       16
D25V5, multiclass
             clus
vv            NRK MUTATED NRK WILD-TYPE
  I OR II NOS           2             8
  STAGE 0               1             5
  STAGE I               2            22
  STAGE IA              1             9
  STAGE IB              4            20
  STAGE II              5            11
  STAGE IIA             2             8
  STAGE IIB             3            11
  STAGE IIC             1             8
  STAGE III             8            24
  STAGE IIIA            3            10
  STAGE IIIB            3            20
  STAGE IIIC            6            40
  STAGE IV              0            16
[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  9
  NRK WILD-TYPE    44 54 43 48
D25V6, multiclass
       clus
vv      NRK MUTATED NRK WILD-TYPE
  T0+T1           8            44
  T2              5            54
  T3             11            43
  T4              9            48
[1] 4 2
[1] TRUE
[1] "dimension of 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   6
  NRK WILD-TYPE 119  41  27  30
D25V7, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  N0          20           119
  N1           7            41
  N2           6            27
  N3           6            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
  NRK MUTATED    39   0   0   0   0
  NRK WILD-TYPE 205   4   3   2   8
D25V8, multiclass
     clus
vv    NRK MUTATED NRK WILD-TYPE
  M0           39           205
  M1            0             4
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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  7
  NRK WILD-TYPE 89 61
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     14    7
  NRK WILD-TYPE   89   61
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO           14            89
  YES           7            61
[1] 2 2
[1] FALSE
D25V10, binary
               cls
clus              0   1
  NRK MUTATED     8  34
  NRK WILD-TYPE  28 205
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED      8   34
  NRK WILD-TYPE   28  205
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO            8            28
  YES          34           205
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, binary
               cls
clus              0   1
  NRK MUTATED    19  24
  NRK WILD-TYPE  87 146
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     19   24
  NRK WILD-TYPE   87  146
        clus
vv       NRK MUTATED NRK WILD-TYPE
  FEMALE          19            87
  MALE            24           146
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRK MUTATED       0                         0    43
  NRK WILD-TYPE     3                         1   229
D25V13, multiclass
                           clus
vv                          NRK MUTATED NRK WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              43           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"
D25V14, binary
               cls
clus              0   1
  NRK MUTATED     0  43
  NRK WILD-TYPE   3 226
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED      0   43
  NRK WILD-TYPE    3  226
                        clus
vv                       NRK MUTATED NRK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          43           226
[1] 2 2
[1] FALSE

Clustering(26) Variable = TAF1A MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  TAF1A MUTATED     4   9
  TAF1A WILD-TYPE 122 131
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             253 
  TAF1A MUTATED TAF1A WILD-TYPE 
              9             131 
$`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        52.67       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        86.76        11.41        44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34        15.85 
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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.16         5.56       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A1ZK 
        8.22        19.53        11.08         7.17        30.87        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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       10.13        16.24        15.42        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  TAF1A MUTATED TAF1A WILD-TYPE 
           1.12            0.13 
  TAF1A MUTATED TAF1A WILD-TYPE 
         124.31          125.65 
  TAF1A MUTATED TAF1A WILD-TYPE 
          13.32           17.72 
[1] "1.1 - 124.3 (13.3)" "0.1 - 125.7 (17.7)"
[1] "hr=" "1.3"
D26V2, survival
                 sevent
clus2               0   1
  TAF1A MUTATED     4   9
  TAF1A WILD-TYPE 125 132
  TAF1A MUTATED TAF1A WILD-TYPE 
             13             257 
  TAF1A MUTATED TAF1A WILD-TYPE 
              9             132 
$`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        71.21       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        86.76        11.87        62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       47.54       248.65        43.23       134.40       162.48        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        32.75        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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        39.58         6.67         0.33         0.69 

  TAF1A MUTATED TAF1A WILD-TYPE 
          12.10            0.16 
  TAF1A MUTATED TAF1A WILD-TYPE 
         124.31          357.37 
  TAF1A MUTATED TAF1A WILD-TYPE 
          50.89           52.01 
[1] "12.1 - 124.3 (50.9)" "0.2 - 357.4 (52.0)" 
[1] "hr=" "1.8"
D26V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  TAF1A MUTATED                    0             0
  TAF1A WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TAF1A MUTATED                                           2                  11
  TAF1A WILD-TYPE                                        58                 160
D26V4, multiclass
                                           clus
vv                                          TAF1A MUTATED TAF1A WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                  11             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
  TAF1A MUTATED             0       0       1        0        3        1
  TAF1A WILD-TYPE          10       6      23       10       21       15
                 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        30         12         23
                 vv
clus              STAGE IIIC STAGE IV
  TAF1A MUTATED            3        0
  TAF1A WILD-TYPE         43       16
D26V5, multiclass
             clus
vv            TAF1A MUTATED TAF1A WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                0              10
  STAGE IB                3              21
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               2              30
  STAGE IIIA              1              12
  STAGE IIIB              0              23
  STAGE IIIC              3              43
  STAGE IV                0              16
[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    49 55 52 55
D26V6, multiclass
       clus
vv      TAF1A MUTATED TAF1A WILD-TYPE
  T0+T1             3              49
  T2                4              55
  T3                2              52
  T4                2              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
  TAF1A MUTATED     7   2   2   2
  TAF1A WILD-TYPE 132  46  31  34
D26V7, multiclass
    clus
vv   TAF1A MUTATED TAF1A WILD-TYPE
  N0             7             132
  N1             2              46
  N2             2              31
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  TAF1A MUTATED    13   0   0   0   0
  TAF1A WILD-TYPE 231   4   3   2   8
D26V8, multiclass
     clus
vv    TAF1A MUTATED TAF1A WILD-TYPE
  M0             13             231
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 96 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      7    3
  TAF1A WILD-TYPE   96   65
     clus
vv    TAF1A MUTATED TAF1A WILD-TYPE
  NO              7              96
  YES             3              65
[1] 2 2
[1] FALSE
D26V10, binary
                 cls
clus                0   1
  TAF1A MUTATED     2  11
  TAF1A WILD-TYPE  34 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      2   11
  TAF1A WILD-TYPE   34  228
     clus
vv    TAF1A MUTATED TAF1A WILD-TYPE
  NO              2              34
  YES            11             228
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, binary
                 cls
clus                0   1
  TAF1A MUTATED     8   5
  TAF1A WILD-TYPE  98 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      8    5
  TAF1A WILD-TYPE   98  165
        clus
vv       TAF1A MUTATED TAF1A WILD-TYPE
  FEMALE             8              98
  MALE               5             165
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAF1A MUTATED       0                         0    13
  TAF1A WILD-TYPE     3                         1   259
D26V13, multiclass
                           clus
vv                          TAF1A MUTATED TAF1A WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             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"
D26V14, binary
                 cls
clus                0   1
  TAF1A MUTATED     0  13
  TAF1A WILD-TYPE   3 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1A MUTATED      0   13
  TAF1A WILD-TYPE    3  256
                        clus
vv                       TAF1A MUTATED TAF1A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             256
[1] 2 2
[1] FALSE

Clustering(27) Variable = OXA1L MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  OXA1L MUTATED     4   4
  OXA1L WILD-TYPE 122 136
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             258 
  OXA1L MUTATED OXA1L WILD-TYPE 
              4             136 
$`OXA1L MUTATED`
TCGA-D3-A51T TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A2GB TCGA-EE-A2MS 
       25.78         4.93         8.12         1.12        51.12        53.16 
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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       54.31        32.28        21.44        32.61        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        60.49        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22         0.95        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  OXA1L MUTATED OXA1L WILD-TYPE 
           0.99            0.13 
  OXA1L MUTATED OXA1L WILD-TYPE 
          53.16          125.65 
  OXA1L MUTATED OXA1L WILD-TYPE 
          16.95           16.90 
[1] "1.0 - 53.2 (16.9)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.2"
D27V2, survival
                 sevent
clus2               0   1
  OXA1L MUTATED     4   4
  OXA1L WILD-TYPE 125 137
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             262 
  OXA1L MUTATED OXA1L WILD-TYPE 
              4             137 
$`OXA1L MUTATED`
TCGA-D3-A51T TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A2GB TCGA-EE-A2MS 
       26.89        65.92        94.98        33.73        59.28       162.48 
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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        32.94        22.62        63.81       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      134.40        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  OXA1L MUTATED OXA1L WILD-TYPE 
          22.92            0.16 
  OXA1L MUTATED OXA1L WILD-TYPE 
         162.48          357.37 
  OXA1L MUTATED OXA1L WILD-TYPE 
         46.505          51.815 
[1] "22.9 - 162.5 (46.5)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1.1"
D27V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  OXA1L MUTATED                    2             0
  OXA1L WILD-TYPE                 37             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  OXA1L MUTATED                                           0                   6
  OXA1L WILD-TYPE                                        60                 165
D27V4, multiclass
                                           clus
vv                                          OXA1L MUTATED OXA1L WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             0              60
  REGIONAL LYMPH NODE                                   6             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
  OXA1L MUTATED             0       0       0        0        0        2
  OXA1L WILD-TYPE          10       6      24       10       24       14
                 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        29         13         21
                 vv
clus              STAGE IIIC STAGE IV
  OXA1L MUTATED            1        0
  OXA1L WILD-TYPE         45       16
D27V5, multiclass
             clus
vv            OXA1L MUTATED OXA1L WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                2              14
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               3              29
  STAGE IIIA              0              13
  STAGE IIIB              2              21
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    52 57 52 55
D27V6, multiclass
       clus
vv      OXA1L MUTATED OXA1L WILD-TYPE
  T0+T1             0              52
  T2                2              57
  T3                2              52
  T4                2              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
  OXA1L MUTATED     3   3   2   0
  OXA1L WILD-TYPE 136  45  31  36
D27V7, multiclass
    clus
vv   OXA1L MUTATED OXA1L WILD-TYPE
  N0             3             136
  N1             3              45
  N2             2              31
  N3             0              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               M0  M1 M1A M1B M1C
  OXA1L MUTATED     8   0   0   0   0
  OXA1L WILD-TYPE 236   4   3   2   8
D27V8, multiclass
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  M0              8             236
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 100  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      3    2
  OXA1L WILD-TYPE  100   66
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  NO              3             100
  YES             2              66
[1] 2 2
[1] FALSE
D27V10, binary
                 cls
clus                0   1
  OXA1L MUTATED     1   7
  OXA1L WILD-TYPE  35 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      1    7
  OXA1L WILD-TYPE   35  232
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  NO              1              35
  YES             7             232
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, binary
                 cls
clus                0   1
  OXA1L MUTATED     3   5
  OXA1L WILD-TYPE 103 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      3    5
  OXA1L WILD-TYPE  103  165
        clus
vv       OXA1L MUTATED OXA1L WILD-TYPE
  FEMALE             3             103
  MALE               5             165
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OXA1L MUTATED       0                         0     8
  OXA1L WILD-TYPE     3                         1   264
D27V13, multiclass
                           clus
vv                          OXA1L MUTATED OXA1L WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             264
[1] 3 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   3 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      0    8
  OXA1L WILD-TYPE    3  261
                        clus
vv                       OXA1L MUTATED OXA1L WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             261
[1] 2 2
[1] FALSE

Clustering(28) Variable = COL3A1 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  COL3A1 MUTATED    26  28
  COL3A1 WILD-TYPE 100 112
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              54              212 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              28              112 
$`COL3A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C7 
       70.16        86.76        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        29.23        52.01        47.87        17.72        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        62.79         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 
       55.69         5.42         8.84        47.51        63.42        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 
       53.16        52.67        51.62        15.95        12.72        21.60 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19F 
        0.95        27.35        18.41        31.40         3.78        11.11 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A4F5 
       34.88         4.21        11.80        14.24        12.89        28.73 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-GN-A266 TCGA-RP-A693 
       10.78         0.99         0.13        11.61        10.13         0.33 

$`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        44.19         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        59.57       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        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 
       21.44        32.61        25.78        13.68        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17Z 
        0.20        23.15        19.00        13.35        13.22         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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       37.97         8.55        36.85        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       11.31        49.22        36.30        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       33.83         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        2.70         6.18         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       26.99        21.60         5.56       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       30.15        13.81         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       22.22        21.73        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G 
        5.72        76.41        25.18         3.52        11.90       114.15 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
        7.36        14.20         5.98         6.41         2.27         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A694 
        5.79         0.69 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            0.13             0.16 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
           86.76           125.65 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          16.755           16.900 
[1] "0.1 - 86.8 (16.8)"  "0.2 - 125.7 (16.9)"
[1] "hr=" "1"  
D28V2, survival
                  sevent
clus2                0   1
  COL3A1 MUTATED    27  28
  COL3A1 WILD-TYPE 102 113
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              55              215 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              28              113 
$`COL3A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3C7 
       71.80        86.76        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        45.30       135.75       137.92        18.18         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        63.78         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       126.81        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 
      134.40       162.48        71.21        51.62        23.47       138.81 
TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A19C 
       36.95       201.80        27.35        51.35        31.40        48.89 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1ZK 
       26.37       152.35         6.44        43.82        20.91        23.93 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-GN-A266 
       28.73        12.43        22.92        47.54        11.74        10.13 
TCGA-RP-A693 
        0.33 

$`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        62.07       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        59.57       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       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 
       22.62        63.81        26.89       178.32       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        22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       17.29        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       133.81       151.27        91.56       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        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       86.14        59.28       314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU 
      203.05       167.90        47.54       248.65        43.23        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73         3.68        54.51        13.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
      127.20        64.08        34.32        53.19       109.58       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-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       12.59        13.02       268.93       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       15.72       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-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-A4F8 TCGA-FS-A4FB 
       27.09        27.02        77.82        66.67       174.84        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45        77.88         0.20         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23         2.04       139.89       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.69 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            0.33             0.16 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          215.44           357.37 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
           43.82            54.51 
[1] "0.3 - 215.4 (43.8)" "0.2 - 357.4 (54.5)"
[1] "hr=" "1.2"
D28V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  COL3A1 MUTATED                    7             1
  COL3A1 WILD-TYPE                 32             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  COL3A1 MUTATED                                          15
  COL3A1 WILD-TYPE                                        45
                  vv
clus               REGIONAL LYMPH NODE
  COL3A1 MUTATED                    33
  COL3A1 WILD-TYPE                 138
D28V4, multiclass
                                           clus
vv                                          COL3A1 MUTATED COL3A1 WILD-TYPE
  DISTANT METASTASIS                                     7               32
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             15               45
  REGIONAL LYMPH NODE                                   33              138
[1] 4 2
[1] 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      19        8       20       10
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  COL3A1 MUTATED           0         2         0        10          2
  COL3A1 WILD-TYPE        10        12         9        22         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  COL3A1 MUTATED            7          9        4
  COL3A1 WILD-TYPE         16         37       12
D28V5, multiclass
             clus
vv            COL3A1 MUTATED COL3A1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  5               19
  STAGE IA                 2                8
  STAGE IB                 4               20
  STAGE II                 6               10
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III               10               22
  STAGE IIIA               2               11
  STAGE IIIB               7               16
  STAGE IIIC               9               37
  STAGE IV                 4               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
  COL3A1 MUTATED      11 10 14 10
  COL3A1 WILD-TYPE    41 49 40 47
D28V6, multiclass
       clus
vv      COL3A1 MUTATED COL3A1 WILD-TYPE
  T0+T1             11               41
  T2                10               49
  T3                14               40
  T4                10               47
[1] 4 2
[1] TRUE
[1] "dimension of 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  13   9   7
  COL3A1 WILD-TYPE 117  35  24  29
D28V7, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  N0             22              117
  N1             13               35
  N2              9               24
  N3              7               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
  COL3A1 MUTATED    49   2   0   0   2
  COL3A1 WILD-TYPE 195   2   3   2   6
D28V8, multiclass
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  M0              49              195
  M1               2                2
  M1A              0                3
  M1B              0                2
  M1C              2                6
[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 82 56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     21   12
  COL3A1 WILD-TYPE   82   56
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO              21               82
  YES             12               56
[1] 2 2
[1] FALSE
D28V10, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    11  45
  COL3A1 WILD-TYPE  25 194
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     11   45
  COL3A1 WILD-TYPE   25  194
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO              11               25
  YES             45              194
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    12  44
  COL3A1 WILD-TYPE  94 126
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     12   44
  COL3A1 WILD-TYPE   94  126
        clus
vv       COL3A1 MUTATED COL3A1 WILD-TYPE
  FEMALE             12               94
  MALE               44              126
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL3A1 MUTATED       1                         0    55
  COL3A1 WILD-TYPE     2                         1   217
D28V13, multiclass
                           clus
vv                          COL3A1 MUTATED COL3A1 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 55              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"
D28V14, binary
                  cls
clus                 0   1
  COL3A1 MUTATED     0  54
  COL3A1 WILD-TYPE   3 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED      0   54
  COL3A1 WILD-TYPE    3  215
                        clus
vv                       COL3A1 MUTATED COL3A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             54              215
[1] 2 2
[1] FALSE

Clustering(29) Variable = TCHHL1 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  TCHHL1 MUTATED    24  13
  TCHHL1 WILD-TYPE 102 127
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              37              229 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              13              127 
$`TCHHL1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T 
       44.19        92.42        46.98        29.23        32.61        25.78 
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 
       62.79         8.55        39.62         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        60.49         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 
TCGA-RP-A694 
        0.69 

$`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        86.76        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        59.57 
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        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       54.74        31.30        54.31        32.28        21.44        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       10.55         6.31         8.12         5.13         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15        36.85         1.08         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       17.98        60.00        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-A2M5 
       33.83        55.69         5.42         1.15        13.02         8.84 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        2.70         6.18         9.53        29.46         2.73        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       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
       25.08        26.99        21.60        53.16        52.67       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB 
        3.22        22.92        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       12.95        38.40         5.72        25.18         3.78        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       11.11        34.88         4.21        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71         5.62        85.74        15.72 
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-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       14.20        10.78         6.41         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 
TCGA-RP-A693 
        0.33 

  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
            0.69             0.13 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
          124.31           125.65 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
           25.78            16.01 
[1] "0.7 - 124.3 (25.8)" "0.1 - 125.7 (16.0)"
[1] "hr=" "1.8"
D29V2, survival
                  sevent
clus2                0   1
  TCHHL1 MUTATED    25  13
  TCHHL1 WILD-TYPE 104 128
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              38              232 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
              13              128 
$`TCHHL1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T 
       62.07       171.58        46.98        45.30        63.81        26.89 
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        63.78        72.07        56.84        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       134.40 
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 TCGA-RP-A694 
       32.48         0.69 

$`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        86.76        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        59.57 
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       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       55.73        56.35       145.12        32.94        22.62       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81       151.27        91.56       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        64.64 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        71.21       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        23.47       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       98.40        48.89        13.02        26.37       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6.77       174.21        15.72       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-A4FC 
       77.82        66.67        28.73       174.84        12.43        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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2.04        11.74       139.89       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       62.79        39.58         6.67         0.33 

  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
            0.69             0.16 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
          268.93           357.37 
  TCHHL1 MUTATED TCHHL1 WILD-TYPE 
          51.075           51.815 
[1] "0.7 - 268.9 (51.1)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.4"
D29V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  TCHHL1 MUTATED                    3             1
  TCHHL1 WILD-TYPE                 36             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  TCHHL1 MUTATED                                          10
  TCHHL1 WILD-TYPE                                        50
                  vv
clus               REGIONAL LYMPH NODE
  TCHHL1 MUTATED                    25
  TCHHL1 WILD-TYPE                 146
D29V4, multiclass
                                           clus
vv                                          TCHHL1 MUTATED TCHHL1 WILD-TYPE
  DISTANT METASTASIS                                     3               36
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               50
  REGIONAL LYMPH NODE                                   25              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
  TCHHL1 MUTATED             1       2       3        5        3        1
  TCHHL1 WILD-TYPE           9       4      21        5       21       15
                  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        27         10
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  TCHHL1 MUTATED            3          3        3
  TCHHL1 WILD-TYPE         20         43       13
D29V5, multiclass
             clus
vv            TCHHL1 MUTATED TCHHL1 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  3               21
  STAGE IA                 5                5
  STAGE IB                 3               21
  STAGE II                 1               15
  STAGE IIA                3                7
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                5               27
  STAGE IIIA               3               10
  STAGE IIIB               3               20
  STAGE IIIC               3               43
  STAGE IV                 3               13
[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    42 51 47 52
D29V6, multiclass
       clus
vv      TCHHL1 MUTATED TCHHL1 WILD-TYPE
  T0+T1             10               42
  T2                 8               51
  T3                 7               47
  T4                 5               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
  TCHHL1 MUTATED    20   8   6   2
  TCHHL1 WILD-TYPE 119  40  27  34
D29V7, multiclass
    clus
vv   TCHHL1 MUTATED TCHHL1 WILD-TYPE
  N0             20              119
  N1              8               40
  N2              6               27
  N3              2               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  TCHHL1 MUTATED    34   1   1   0   1
  TCHHL1 WILD-TYPE 210   3   2   2   7
D29V8, multiclass
     clus
vv    TCHHL1 MUTATED TCHHL1 WILD-TYPE
  M0              34              210
  M1               1                3
  M1A              1                2
  M1B              0                2
  M1C              1                7
[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 82 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED     21    4
  TCHHL1 WILD-TYPE   82   64
     clus
vv    TCHHL1 MUTATED TCHHL1 WILD-TYPE
  NO              21               82
  YES              4               64
[1] 2 2
[1] FALSE
D29V10, binary
                  cls
clus                 0   1
  TCHHL1 MUTATED     7  32
  TCHHL1 WILD-TYPE  29 207
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED      7   32
  TCHHL1 WILD-TYPE   29  207
     clus
vv    TCHHL1 MUTATED TCHHL1 WILD-TYPE
  NO               7               29
  YES             32              207
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, binary
                  cls
clus                 0   1
  TCHHL1 MUTATED    14  25
  TCHHL1 WILD-TYPE  92 145
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED     14   25
  TCHHL1 WILD-TYPE   92  145
        clus
vv       TCHHL1 MUTATED TCHHL1 WILD-TYPE
  FEMALE             14               92
  MALE               25              145
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCHHL1 MUTATED       0                         0    39
  TCHHL1 WILD-TYPE     3                         1   233
D29V13, multiclass
                           clus
vv                          TCHHL1 MUTATED TCHHL1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 39              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"
D29V14, binary
                  cls
clus                 0   1
  TCHHL1 MUTATED     0  39
  TCHHL1 WILD-TYPE   3 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCHHL1 MUTATED      0   39
  TCHHL1 WILD-TYPE    3  230
                        clus
vv                       TCHHL1 MUTATED TCHHL1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             39              230
[1] 2 2
[1] FALSE

Clustering(30) Variable = IL5RA MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  IL5RA MUTATED     8   9
  IL5RA WILD-TYPE 118 131
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             249 
  IL5RA MUTATED IL5RA WILD-TYPE 
              9             131 
$`IL5RA MUTATED`
TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2MJ 
       25.78        11.57        10.55        62.79         1.08        63.42 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A193 
       60.49        53.16        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       54.31        32.28        21.44        32.61        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       13.22         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        60.23         4.34        15.85         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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56       125.65       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        52.67         5.56       124.31       122.73        51.62 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19F TCGA-ER-A19G TCGA-ER-A19H 
       25.18         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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       14.20        10.78         5.98         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  IL5RA MUTATED IL5RA WILD-TYPE 
           0.99            0.13 
  IL5RA MUTATED IL5RA WILD-TYPE 
          63.42          125.65 
  IL5RA MUTATED IL5RA WILD-TYPE 
          21.60           16.47 
[1] "1.0 - 63.4 (21.6)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.1"
D30V2, survival
                 sevent
clus2               0   1
  IL5RA MUTATED     8   9
  IL5RA WILD-TYPE 121 132
  IL5RA MUTATED IL5RA WILD-TYPE 
             17             253 
  IL5RA MUTATED IL5RA WILD-TYPE 
              9             132 
$`IL5RA MUTATED`
TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2MJ 
       26.89        29.82        27.22        63.78         2.60        96.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A193 
      134.40       162.48        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        32.94        22.62        63.81       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        64.64        56.84 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      203.05       167.90        47.54       248.65        43.23        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        51.62         3.68        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19       201.80        51.35       109.58       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-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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73         0.20        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  IL5RA MUTATED IL5RA WILD-TYPE 
           2.60            0.16 
  IL5RA MUTATED IL5RA WILD-TYPE 
         162.48          357.37 
  IL5RA MUTATED IL5RA WILD-TYPE 
          36.95           53.19 
[1] "2.6 - 162.5 (37.0)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.4"
D30V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  IL5RA MUTATED                    0             0
  IL5RA WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  IL5RA MUTATED                                           4                  13
  IL5RA WILD-TYPE                                        56                 158
D30V4, multiclass
                                           clus
vv                                          IL5RA MUTATED IL5RA WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              56
  REGIONAL LYMPH NODE                                  13             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
  IL5RA MUTATED             0       0       2        2        0        1
  IL5RA WILD-TYPE          10       6      22        8       24       15
                 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        28         13         21
                 vv
clus              STAGE IIIC STAGE IV
  IL5RA MUTATED            3        0
  IL5RA WILD-TYPE         43       16
D30V5, multiclass
             clus
vv            IL5RA MUTATED IL5RA WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              22
  STAGE IA                2               8
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               1               9
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               4              28
  STAGE IIIA              0              13
  STAGE IIIB              2              21
  STAGE IIIC              3              43
  STAGE IV                0              16
[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    50 56 49 53
D30V6, multiclass
       clus
vv      IL5RA MUTATED IL5RA WILD-TYPE
  T0+T1             2              50
  T2                3              56
  T3                5              49
  T4                4              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
  IL5RA MUTATED     7   4   2   2
  IL5RA WILD-TYPE 132  44  31  34
D30V7, multiclass
    clus
vv   IL5RA MUTATED IL5RA WILD-TYPE
  N0             7             132
  N1             4              44
  N2             2              31
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  IL5RA MUTATED    16   0   0   0   0
  IL5RA WILD-TYPE 228   4   3   2   8
D30V8, multiclass
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  M0             16             228
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 93 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED     10    3
  IL5RA WILD-TYPE   93   65
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  NO             10              93
  YES             3              65
[1] 2 2
[1] FALSE
D30V10, binary
                 cls
clus                0   1
  IL5RA MUTATED     2  15
  IL5RA WILD-TYPE  34 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      2   15
  IL5RA WILD-TYPE   34  224
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  NO              2              34
  YES            15             224
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, binary
                 cls
clus                0   1
  IL5RA MUTATED     3  14
  IL5RA WILD-TYPE 103 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      3   14
  IL5RA WILD-TYPE  103  156
        clus
vv       IL5RA MUTATED IL5RA WILD-TYPE
  FEMALE             3             103
  MALE              14             156
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL5RA MUTATED       1                         0    16
  IL5RA WILD-TYPE     2                         1   256
D30V13, multiclass
                           clus
vv                          IL5RA MUTATED IL5RA WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                16             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"
D30V14, binary
                 cls
clus                0   1
  IL5RA MUTATED     0  15
  IL5RA WILD-TYPE   3 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      0   15
  IL5RA WILD-TYPE    3  254
                        clus
vv                       IL5RA MUTATED IL5RA WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            15             254
[1] 2 2
[1] FALSE

Clustering(31) Variable = NBPF7 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  NBPF7 MUTATED     8   5
  NBPF7 WILD-TYPE 118 135
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             253 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
              5             135 
$`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        86.76        23.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A29E TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A3J5 
        9.90        13.22        62.79        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        44.19         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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87        13.68        17.72         4.01        21.93 
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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  NBPF7 MUTATED NBPF7 WILD-TYPE 
           0.99            0.13 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
          86.76          125.65 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
          21.60           16.14 
[1] "1.0 - 86.8 (21.6)"  "0.1 - 125.7 (16.1)"
[1] "hr=" "1.7"
D31V2, survival
                 sevent
clus2               0   1
  NBPF7 MUTATED     8   5
  NBPF7 WILD-TYPE 121 136
  NBPF7 MUTATED NBPF7 WILD-TYPE 
             13             257 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
              5             136 
$`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        86.76       125.19 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A29E TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A3J5 
        9.90        66.25        63.78        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        62.07       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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       178.32        18.18       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        22.29        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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB 
      172.18       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  NBPF7 MUTATED NBPF7 WILD-TYPE 
           9.90            0.16 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
         125.19          357.37 
  NBPF7 MUTATED NBPF7 WILD-TYPE 
          63.78           51.62 
[1] "9.9 - 125.2 (63.8)" "0.2 - 357.4 (51.6)"
[1] "hr=" "1.2"
D31V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NBPF7 MUTATED                    0             2
  NBPF7 WILD-TYPE                 39             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NBPF7 MUTATED                                           1                  10
  NBPF7 WILD-TYPE                                        59                 161
D31V4, multiclass
                                           clus
vv                                          NBPF7 MUTATED NBPF7 WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         2               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                  10             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
  NBPF7 MUTATED             0       0       0        0        2        0
  NBPF7 WILD-TYPE          10       6      24       10       22       16
                 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        27         10         22
                 vv
clus              STAGE IIIC STAGE IV
  NBPF7 MUTATED            1        0
  NBPF7 WILD-TYPE         45       16
D31V5, multiclass
             clus
vv            NBPF7 MUTATED NBPF7 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              27
  STAGE IIIA              3              10
  STAGE IIIB              1              22
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    48 58 49 55
D31V6, multiclass
       clus
vv      NBPF7 MUTATED NBPF7 WILD-TYPE
  T0+T1             4              48
  T2                1              58
  T3                5              49
  T4                2              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
  NBPF7 MUTATED     4   4   4   1
  NBPF7 WILD-TYPE 135  44  29  35
D31V7, multiclass
    clus
vv   NBPF7 MUTATED NBPF7 WILD-TYPE
  N0             4             135
  N1             4              44
  N2             4              29
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NBPF7 MUTATED    13   0   0   0   0
  NBPF7 WILD-TYPE 231   4   3   2   8
D31V8, multiclass
     clus
vv    NBPF7 MUTATED NBPF7 WILD-TYPE
  M0             13             231
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 94 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      9    1
  NBPF7 WILD-TYPE   94   67
     clus
vv    NBPF7 MUTATED NBPF7 WILD-TYPE
  NO              9              94
  YES             1              67
[1] 2 2
[1] FALSE
D31V10, binary
                 cls
clus                0   1
  NBPF7 MUTATED     2  11
  NBPF7 WILD-TYPE  34 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      2   11
  NBPF7 WILD-TYPE   34  228
     clus
vv    NBPF7 MUTATED NBPF7 WILD-TYPE
  NO              2              34
  YES            11             228
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, binary
                 cls
clus                0   1
  NBPF7 MUTATED     6   7
  NBPF7 WILD-TYPE 100 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      6    7
  NBPF7 WILD-TYPE  100  163
        clus
vv       NBPF7 MUTATED NBPF7 WILD-TYPE
  FEMALE             6             100
  MALE               7             163
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF7 MUTATED       0                         0    13
  NBPF7 WILD-TYPE     3                         1   259
D31V13, multiclass
                           clus
vv                          NBPF7 MUTATED NBPF7 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             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"
D31V14, binary
                 cls
clus                0   1
  NBPF7 MUTATED     0  13
  NBPF7 WILD-TYPE   3 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF7 MUTATED      0   13
  NBPF7 WILD-TYPE    3  256
                        clus
vv                       NBPF7 MUTATED NBPF7 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             256
[1] 2 2
[1] FALSE

Clustering(32) Variable = KEL MUTATION ANALYSIS
D32V1, survival
               sevent
clus2             0   1
  KEL MUTATED    19  17
  KEL WILD-TYPE 107 123
  KEL MUTATED KEL WILD-TYPE 
           36           230 
  KEL MUTATED KEL WILD-TYPE 
           17           123 
$`KEL MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A6EC 
       44.19        92.42         6.31       103.59        47.87        13.22 
TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       14.83        13.35        13.22        11.57         1.12         1.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD 
       37.97        11.15        30.08         1.15        36.33         9.53 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 
       63.42        60.49        52.67        13.81        15.95        21.60 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A3PL TCGA-FR-A44A 
       22.22        33.60        18.61        38.40         1.71        85.74 
TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
        5.23         0.99         0.16        11.61        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        86.76        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        59.57 
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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       25.78        52.01        13.68        17.72        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       21.93         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        23.15        19.00        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       51.12        34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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 
       53.16         5.56       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       30.15        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 
        0.95        27.35        18.41        21.73        31.40        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-A42K TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         5.62        18.41 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.13        17.33         9.90         7.23         0.85        44.28 
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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  KEL MUTATED KEL WILD-TYPE 
         0.16          0.13 
  KEL MUTATED KEL WILD-TYPE 
       103.59        125.65 
  KEL MUTATED KEL WILD-TYPE 
       15.390        17.445 
[1] "0.2 - 103.6 (15.4)" "0.1 - 125.7 (17.4)"
[1] "hr=" "1.2"
D32V2, survival
               sevent
clus2             0   1
  KEL MUTATED    19  17
  KEL WILD-TYPE 110 124
  KEL MUTATED KEL WILD-TYPE 
           36           234 
  KEL MUTATED KEL WILD-TYPE 
           17           124 
$`KEL MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A6EC 
       62.07       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        17.29        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       134.40        71.21        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-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
       27.02        22.92         0.16        11.74        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        86.76        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        59.57 
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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       26.89       135.75       178.32        18.18       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        22.29         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        68.25        54.02        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       133.81       151.27        91.56 
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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH 
      124.31       122.73        51.62         3.68        54.51       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       109.58        31.40        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW 
       80.32        46.98         6.77        92.98        15.72       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-A3TU TCGA-FW-A5DY 
       26.73        49.45        77.88         0.20        47.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        9.90         7.23         2.04       139.89       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  KEL MUTATED KEL WILD-TYPE 
         0.16          0.20 
  KEL MUTATED KEL WILD-TYPE 
       174.21        357.37 
  KEL MUTATED KEL WILD-TYPE 
       42.115        53.970 
[1] "0.2 - 174.2 (42.1)" "0.2 - 357.4 (54.0)"
[1] "hr=" "1.2"
D32V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  KEL MUTATED                    6             1
  KEL WILD-TYPE                 33             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KEL MUTATED                                           7                  22
  KEL WILD-TYPE                                        53                 149
D32V4, multiclass
                                           clus
vv                                          KEL MUTATED KEL WILD-TYPE
  DISTANT METASTASIS                                  6            33
  PRIMARY TUMOR                                       1             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           7            53
  REGIONAL LYMPH NODE                                22           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
  KEL MUTATED             1       0       2        4        3        5
  KEL WILD-TYPE           9       6      22        6       21       11
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KEL MUTATED           0         1         1         7          2          2
  KEL WILD-TYPE        10        13         8        25         11         21
               vv
clus            STAGE IIIC STAGE IV
  KEL MUTATED            3        1
  KEL WILD-TYPE         43       15
D32V5, multiclass
             clus
vv            KEL MUTATED KEL WILD-TYPE
  I OR II NOS           1             9
  STAGE 0               0             6
  STAGE I               2            22
  STAGE IA              4             6
  STAGE IB              3            21
  STAGE II              5            11
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             1             8
  STAGE III             7            25
  STAGE IIIA            2            11
  STAGE IIIB            2            21
  STAGE IIIC            3            43
  STAGE IV              1            15
[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    44 53 46 51
D32V6, multiclass
       clus
vv      KEL MUTATED KEL WILD-TYPE
  T0+T1           8            44
  T2              6            53
  T3              8            46
  T4              6            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
  KEL MUTATED    19   6   5   1
  KEL WILD-TYPE 120  42  28  35
D32V7, multiclass
    clus
vv   KEL MUTATED KEL WILD-TYPE
  N0          19           120
  N1           6            42
  N2           5            28
  N3           1            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  KEL MUTATED    32   0   1   0   0
  KEL WILD-TYPE 212   4   2   2   8
D32V8, multiclass
     clus
vv    KEL MUTATED KEL WILD-TYPE
  M0           32           212
  M1            0             4
  M1A           1             2
  M1B           0             2
  M1C           0             8
[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 88 61
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED     15    7
  KEL WILD-TYPE   88   61
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO           15            88
  YES           7            61
[1] 2 2
[1] FALSE
D32V10, binary
               cls
clus              0   1
  KEL MUTATED     6  30
  KEL WILD-TYPE  30 209
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      6   30
  KEL WILD-TYPE   30  209
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO            6            30
  YES          30           209
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, binary
               cls
clus              0   1
  KEL MUTATED     9  27
  KEL WILD-TYPE  97 143
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      9   27
  KEL WILD-TYPE   97  143
        clus
vv       KEL MUTATED KEL WILD-TYPE
  FEMALE           9            97
  MALE            27           143
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KEL MUTATED       0                         0    36
  KEL WILD-TYPE     3                         1   236
D32V13, multiclass
                           clus
vv                          KEL MUTATED KEL WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              36           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"
D32V14, binary
               cls
clus              0   1
  KEL MUTATED     1  34
  KEL WILD-TYPE   2 235
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      1   34
  KEL WILD-TYPE    2  235
                        clus
vv                       KEL MUTATED KEL WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          34           235
[1] 2 2
[1] FALSE

Clustering(33) Variable = C7ORF58 MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    16  16
  C7ORF58 WILD-TYPE 110 124
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               32               234 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               16               124 
$`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 
       62.79        12.03        51.12        55.69         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        60.49       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-GF-A6C9 TCGA-GN-A267 TCGA-GN-A268 
       20.38         5.98         0.99        11.61        16.24        15.42 
TCGA-GN-A26A TCGA-RP-A693 
       12.16         0.33 

$`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        86.76        11.41        44.19 
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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50         8.09         8.84         9.99         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        28.31        33.83         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       34.98         8.84        98.27         6.18        47.51        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG 
       52.67         5.56       122.73        51.62         3.68        15.95 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
        3.22        21.60        16.14        22.22         0.95        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       21.73        33.60        18.61        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        64.47         3.45        11.01        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-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-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       14.20        10.78         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        17.33         9.90         7.23         0.85        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       31.33        84.72        10.13        14.70         5.79         0.69 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             0.33              0.13 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           124.31            125.65 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           20.990            16.305 
[1] "0.3 - 124.3 (21.0)" "0.1 - 125.7 (16.3)"
[1] "hr=" "1.1"
D33V2, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    17  16
  C7ORF58 WILD-TYPE 112 125
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               33               237 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               16               125 
$`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        63.78        56.42        59.28       126.81        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       134.40       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-GF-A6C9 TCGA-GN-A267 
       50.76       357.37        26.73        22.92        11.74        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-RP-A693 
       62.79        32.48         0.33 

$`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        86.76        11.87        62.07 
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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       135.75       178.32        18.18 
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        22.29 
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        68.25        54.02        17.29        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       133.81       151.27        91.56       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 
       64.64         2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        67.43       314.56       161.03 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       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       158.63       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       162.48        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 
       51.62         3.68        23.47       172.18        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19       201.80        51.35       109.58       148.08        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-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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-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-A4FC 
       77.82        66.67        28.73       174.84        12.43        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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         2.04       139.89       117.93        84.72        10.13 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       39.58         6.67         0.69 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             0.33              0.16 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           357.37            314.56 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
            54.51             51.62 
[1] "0.3 - 357.4 (54.5)" "0.2 - 314.6 (51.6)"
[1] "hr=" "1.1"
D33V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  C7ORF58 MUTATED                    5             0
  C7ORF58 WILD-TYPE                 34             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C7ORF58 MUTATED                                           8
  C7ORF58 WILD-TYPE                                        52
                   vv
clus                REGIONAL LYMPH NODE
  C7ORF58 MUTATED                    21
  C7ORF58 WILD-TYPE                 150
D33V4, multiclass
                                           clus
vv                                          C7ORF58 MUTATED C7ORF58 WILD-TYPE
  DISTANT METASTASIS                                      5                34
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               8                52
  REGIONAL LYMPH NODE                                    21               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
  C7ORF58 MUTATED             2       0       2        2        0        6
  C7ORF58 WILD-TYPE           8       6      22        8       24       10
                   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        27         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C7ORF58 MUTATED            6          2        2
  C7ORF58 WILD-TYPE         17         44       14
D33V5, multiclass
             clus
vv            C7ORF58 MUTATED C7ORF58 WILD-TYPE
  I OR II NOS               2                 8
  STAGE 0                   0                 6
  STAGE I                   2                22
  STAGE IA                  2                 8
  STAGE IB                  0                24
  STAGE II                  6                10
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 1                 8
  STAGE III                 5                27
  STAGE IIIA                2                11
  STAGE IIIB                6                17
  STAGE IIIC                2                44
  STAGE IV                  2                14
[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    45 53 46 51
D33V6, multiclass
       clus
vv      C7ORF58 MUTATED C7ORF58 WILD-TYPE
  T0+T1               7                45
  T2                  6                53
  T3                  8                46
  T4                  6                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
  C7ORF58 MUTATED    15   9   5   2
  C7ORF58 WILD-TYPE 124  39  28  34
D33V7, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  N0              15               124
  N1               9                39
  N2               5                28
  N3               2                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  C7ORF58 MUTATED    31   0   1   0   1
  C7ORF58 WILD-TYPE 213   4   2   2   7
D33V8, multiclass
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  M0               31               213
  M1                0                 4
  M1A               1                 2
  M1B               0                 2
  M1C               1                 7
[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 92 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     11    9
  C7ORF58 WILD-TYPE   92   59
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO               11                92
  YES               9                59
[1] 2 2
[1] FALSE
D33V10, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     8  26
  C7ORF58 WILD-TYPE  28 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      8   26
  C7ORF58 WILD-TYPE   28  213
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO                8                28
  YES              26               213
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    13  21
  C7ORF58 WILD-TYPE  93 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     13   21
  C7ORF58 WILD-TYPE   93  149
        clus
vv       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  FEMALE              13                93
  MALE                21               149
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C7ORF58 MUTATED       0                         0    34
  C7ORF58 WILD-TYPE     3                         1   238
D33V13, multiclass
                           clus
vv                          C7ORF58 MUTATED C7ORF58 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  34               238
[1] 3 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  34
  C7ORF58 WILD-TYPE   3 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      0   34
  C7ORF58 WILD-TYPE    3  235
                        clus
vv                       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              34               235
[1] 2 2
[1] FALSE

Clustering(34) Variable = NBPF1 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  NBPF1 MUTATED    18  20
  NBPF1 WILD-TYPE 108 120
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             38             228 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             20             120 
$`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        86.76        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 
       15.85        11.15        62.79        36.85         1.08         9.99 
TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MR 
       51.12        33.83        55.69         1.15        98.27        60.49 
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-GF-A6C9 
       11.11       114.15         7.30        12.89         0.99        11.61 
TCGA-GN-A265 TCGA-GN-A266 
       84.72        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        44.19         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        59.57       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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       25.78        52.01        47.87        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY 
        4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        13.22 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       10.55         6.31         8.12        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       60.23         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55        39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        36.33        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP 
       30.08        19.43        16.01        35.54        28.31         5.42 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33         8.84         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        53.16        52.67         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62        30.15        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19H TCGA-ER-A19J 
       25.18         3.78         3.52        11.90        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        9.90         7.23         0.85        44.28        31.33        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
           0.99            0.13 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         124.31          125.65 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         13.515          17.640 
[1] "1.0 - 124.3 (13.5)" "0.1 - 125.7 (17.6)"
[1] "hr=" "1.1"
D34V2, survival
                 sevent
clus2               0   1
  NBPF1 MUTATED    18  20
  NBPF1 WILD-TYPE 111 121
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             38             232 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             20             121 
$`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        86.76        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 
       91.56        13.97        63.78        64.64         2.60        55.92 
TCGA-EE-A2GB TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MR 
       59.28        90.97       126.81        14.30       129.27       134.40 
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-GF-A6C9 
       26.37       268.93        27.72        23.93        22.92        11.74 
TCGA-GN-A265 TCGA-GN-A266 
       84.72        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        62.07       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        59.57       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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       135.75       137.92       178.32        18.18       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        22.29 
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 
       68.25        54.02        17.29        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       133.81       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        56.84 
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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      162.48        71.21        53.26       122.73        51.62        54.51 
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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       53.19       201.80        51.35       109.58        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59        13.02       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        2.04       139.89       117.93        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
           2.60            0.16 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         268.93          357.37 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         52.405          51.815 
[1] "2.6 - 268.9 (52.4)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.2"
D34V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NBPF1 MUTATED                    5             1
  NBPF1 WILD-TYPE                 34             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NBPF1 MUTATED                                           8                  25
  NBPF1 WILD-TYPE                                        52                 146
D34V4, multiclass
                                           clus
vv                                          NBPF1 MUTATED NBPF1 WILD-TYPE
  DISTANT METASTASIS                                    5              34
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             8              52
  REGIONAL LYMPH NODE                                  25             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
  NBPF1 MUTATED             0       2       5        2        1        4
  NBPF1 WILD-TYPE          10       4      19        8       23       12
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NBPF1 MUTATED           2         1         0         5          2          6
  NBPF1 WILD-TYPE         8        13         9        27         11         17
                 vv
clus              STAGE IIIC STAGE IV
  NBPF1 MUTATED            5        0
  NBPF1 WILD-TYPE         41       16
D34V5, multiclass
             clus
vv            NBPF1 MUTATED NBPF1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 2               4
  STAGE I                 5              19
  STAGE IA                2               8
  STAGE IB                1              23
  STAGE II                4              12
  STAGE IIA               2               8
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              27
  STAGE IIIA              2              11
  STAGE IIIB              6              17
  STAGE IIIC              5              41
  STAGE IV                0              16
[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    42 52 46 52
D34V6, multiclass
       clus
vv      NBPF1 MUTATED NBPF1 WILD-TYPE
  T0+T1            10              42
  T2                7              52
  T3                8              46
  T4                5              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
  NBPF1 MUTATED    19   7   8   2
  NBPF1 WILD-TYPE 120  41  25  34
D34V7, multiclass
    clus
vv   NBPF1 MUTATED NBPF1 WILD-TYPE
  N0            19             120
  N1             7              41
  N2             8              25
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NBPF1 MUTATED    36   0   0   0   0
  NBPF1 WILD-TYPE 208   4   3   2   8
D34V8, multiclass
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  M0             36             208
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 91 59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     12    9
  NBPF1 WILD-TYPE   91   59
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO             12              91
  YES             9              59
[1] 2 2
[1] FALSE
D34V10, binary
                 cls
clus                0   1
  NBPF1 MUTATED    10  29
  NBPF1 WILD-TYPE  26 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     10   29
  NBPF1 WILD-TYPE   26  210
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO             10              26
  YES            29             210
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, binary
                 cls
clus                0   1
  NBPF1 MUTATED    10  29
  NBPF1 WILD-TYPE  96 141
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     10   29
  NBPF1 WILD-TYPE   96  141
        clus
vv       NBPF1 MUTATED NBPF1 WILD-TYPE
  FEMALE            10              96
  MALE              29             141
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF1 MUTATED       0                         0    39
  NBPF1 WILD-TYPE     3                         1   233
D34V13, multiclass
                           clus
vv                          NBPF1 MUTATED NBPF1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                39             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"
D34V14, binary
                 cls
clus                0   1
  NBPF1 MUTATED     0  38
  NBPF1 WILD-TYPE   3 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      0   38
  NBPF1 WILD-TYPE    3  231
                        clus
vv                       NBPF1 MUTATED NBPF1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            38             231
[1] 2 2
[1] FALSE

Clustering(35) Variable = TMEM216 MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  TMEM216 MUTATED     3   5
  TMEM216 WILD-TYPE 123 135
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               258 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                5               135 
$`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        36.33         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        86.76        11.41        44.19 
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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        13.22        11.57 
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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30         9.67        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        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        55.69         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-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        17.72        78.44        11.80 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  TMEM216 MUTATED TMEM216 WILD-TYPE 
             1.15              0.13 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
            82.29            125.65 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
           18.445            16.900 
[1] "1.1 - 82.3 (18.4)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.1"
D35V2, survival
                   sevent
clus2                 0   1
  TMEM216 MUTATED     3   5
  TMEM216 WILD-TYPE 126 136
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                8               262 
  TMEM216 MUTATED TMEM216 WILD-TYPE 
                5               136 
$`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        86.14        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        86.76        11.87        62.07 
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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       31.27       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  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            51.815 
[1] "14.3 - 166.5 (43.0)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1.5"
D35V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  TMEM216 MUTATED                    1             0
  TMEM216 WILD-TYPE                 38             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  TMEM216 MUTATED                                           4
  TMEM216 WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  TMEM216 MUTATED                     3
  TMEM216 WILD-TYPE                 168
D35V4, multiclass
                                           clus
vv                                          TMEM216 MUTATED TMEM216 WILD-TYPE
  DISTANT METASTASIS                                      1                38
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                56
  REGIONAL LYMPH NODE                                     3               168
[1] 4 2
[1] 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      24        9       24       15
                   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        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  TMEM216 MUTATED            1          3        0
  TMEM216 WILD-TYPE         22         43       16
D35V5, multiclass
             clus
vv            TMEM216 MUTATED TMEM216 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   0                24
  STAGE IA                  1                 9
  STAGE IB                  0                24
  STAGE II                  1                15
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 1                31
  STAGE IIIA                0                13
  STAGE IIIB                1                22
  STAGE IIIC                3                43
  STAGE IV                  0                16
[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    50 58 53 53
D35V6, multiclass
       clus
vv      TMEM216 MUTATED TMEM216 WILD-TYPE
  T0+T1               2                50
  T2                  1                58
  T3                  1                53
  T4                  4                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
  TMEM216 MUTATED     3   2   0   3
  TMEM216 WILD-TYPE 136  46  33  33
D35V7, multiclass
    clus
vv   TMEM216 MUTATED TMEM216 WILD-TYPE
  N0               3               136
  N1               2                46
  N2               0                33
  N3               3                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
  TMEM216 MUTATED     8   0   0   0   0
  TMEM216 WILD-TYPE 236   4   3   2   8
D35V8, multiclass
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  M0                8               236
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 100  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      3    2
  TMEM216 WILD-TYPE  100   66
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  NO                3               100
  YES               2                66
[1] 2 2
[1] FALSE
D35V10, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     0   8
  TMEM216 WILD-TYPE  36 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    8
  TMEM216 WILD-TYPE   36  231
     clus
vv    TMEM216 MUTATED TMEM216 WILD-TYPE
  NO                0                36
  YES               8               231
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     2   6
  TMEM216 WILD-TYPE 104 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      2    6
  TMEM216 WILD-TYPE  104  164
        clus
vv       TMEM216 MUTATED TMEM216 WILD-TYPE
  FEMALE               2               104
  MALE                 6               164
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM216 MUTATED       1                         0     7
  TMEM216 WILD-TYPE     2                         1   265
D35V13, multiclass
                           clus
vv                          TMEM216 MUTATED TMEM216 WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7               265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                   cls
clus                  0   1
  TMEM216 MUTATED     0   7
  TMEM216 WILD-TYPE   3 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM216 MUTATED      0    7
  TMEM216 WILD-TYPE    3  262
                        clus
vv                       TMEM216 MUTATED TMEM216 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               262
[1] 2 2
[1] FALSE

Clustering(36) Variable = DOM3Z MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  DOM3Z MUTATED     2   4
  DOM3Z WILD-TYPE 124 136
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              6             260 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              4             136 
$`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        86.76        11.41        44.19         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        59.57       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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       25.78        52.01        47.87        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01        21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        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 
       60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  DOM3Z MUTATED DOM3Z WILD-TYPE 
           1.08            0.13 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
          45.83          125.65 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
         14.235          17.640 
[1] "1.1 - 45.8 (14.2)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.7"
D36V2, survival
                 sevent
clus2               0   1
  DOM3Z MUTATED     3   4
  DOM3Z WILD-TYPE 126 137
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              7             263 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
              4             137 
$`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        86.76        11.87        62.07       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        59.57       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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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 
       63.78        72.07        64.64        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  DOM3Z MUTATED DOM3Z WILD-TYPE 
           2.60            0.16 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
          90.90          357.37 
  DOM3Z MUTATED DOM3Z WILD-TYPE 
          54.67           51.62 
[1] "2.6 - 90.9 (54.7)"  "0.2 - 357.4 (51.6)"
[1] "hr=" "1.8"
D36V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DOM3Z MUTATED                    0             1
  DOM3Z WILD-TYPE                 39             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DOM3Z MUTATED                                           1                   5
  DOM3Z WILD-TYPE                                        59                 166
D36V4, multiclass
                                           clus
vv                                          DOM3Z MUTATED DOM3Z WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                   5             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
  DOM3Z MUTATED             0       0       0        0        2        0
  DOM3Z WILD-TYPE          10       6      24       10       22       16
                 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        32         12         23
                 vv
clus              STAGE IIIC STAGE IV
  DOM3Z MUTATED            3        0
  DOM3Z WILD-TYPE         43       16
D36V5, multiclass
             clus
vv            DOM3Z MUTATED DOM3Z WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               0              32
  STAGE IIIA              1              12
  STAGE IIIB              0              23
  STAGE IIIC              3              43
  STAGE IV                0              16
[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    51 57 53 55
D36V6, multiclass
       clus
vv      DOM3Z MUTATED DOM3Z WILD-TYPE
  T0+T1             1              51
  T2                2              57
  T3                1              53
  T4                2              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
  DOM3Z MUTATED     2   2   1   2
  DOM3Z WILD-TYPE 137  46  32  34
D36V7, multiclass
    clus
vv   DOM3Z MUTATED DOM3Z WILD-TYPE
  N0             2             137
  N1             2              46
  N2             1              32
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DOM3Z MUTATED     7   0   0   0   0
  DOM3Z WILD-TYPE 237   4   3   2   8
D36V8, multiclass
     clus
vv    DOM3Z MUTATED DOM3Z WILD-TYPE
  M0              7             237
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 98 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      5    2
  DOM3Z WILD-TYPE   98   66
     clus
vv    DOM3Z MUTATED DOM3Z WILD-TYPE
  NO              5              98
  YES             2              66
[1] 2 2
[1] FALSE
D36V10, binary
                 cls
clus                0   1
  DOM3Z MUTATED     0   7
  DOM3Z WILD-TYPE  36 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      0    7
  DOM3Z WILD-TYPE   36  232
     clus
vv    DOM3Z MUTATED DOM3Z WILD-TYPE
  NO              0              36
  YES             7             232
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, binary
                 cls
clus                0   1
  DOM3Z MUTATED     4   3
  DOM3Z WILD-TYPE 102 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      4    3
  DOM3Z WILD-TYPE  102  167
        clus
vv       DOM3Z MUTATED DOM3Z WILD-TYPE
  FEMALE             4             102
  MALE               3             167
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DOM3Z MUTATED       0                         0     7
  DOM3Z WILD-TYPE     3                         1   265
D36V13, multiclass
                           clus
vv                          DOM3Z MUTATED DOM3Z WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 7             265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                 cls
clus                0   1
  DOM3Z MUTATED     0   7
  DOM3Z WILD-TYPE   3 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOM3Z MUTATED      0    7
  DOM3Z WILD-TYPE    3  262
                        clus
vv                       DOM3Z MUTATED DOM3Z WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7             262
[1] 2 2
[1] FALSE

Clustering(37) Variable = BCLAF1 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED    22  25
  BCLAF1 WILD-TYPE 104 115
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              47              219 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              25              115 
$`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        25.78 
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        62.79         1.08        39.62 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ 
       11.31        36.30        36.33        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        53.16 
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-GF-A6C9 TCGA-GN-A266 TCGA-RP-A693 
        0.13         9.90        11.61        10.13         0.33 

$`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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       31.30        54.31        32.28        21.44        32.61        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW 
       13.68        17.72        23.11        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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-A20F 
        1.35        12.20         5.13         4.31        60.23        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        9.21         1.18         7.99        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       36.85         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB 
        2.43        32.15         8.09        49.22         9.67        51.12 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        47.21        30.08        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       33.83        55.69        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        29.46         2.73        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       125.65       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        60.49        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        51.62         3.68        30.15        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       18.41        21.73        31.40        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-A19M TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
        9.57        36.07         6.58        17.72        78.44         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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       64.47         3.45        11.01        23.80        15.52         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-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-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
        2.27         0.20         0.16        17.33         7.23         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       14.70         5.79         0.69 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            0.13             0.16 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          103.59           125.65 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           13.81            17.72 
[1] "0.1 - 103.6 (13.8)" "0.2 - 125.7 (17.7)"
[1] "hr=" "1.1"
D37V2, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED    23  25
  BCLAF1 WILD-TYPE 106 116
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              48              222 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              25              116 
$`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        26.89 
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        63.78         2.60 
TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       56.84        46.82        36.82        86.14        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 
      162.48        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-GF-A6C9 TCGA-GN-A266 TCGA-RP-A693 
       22.92        47.54         9.90        11.74        10.13         0.33 

$`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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       56.35       145.12        32.94        22.62        63.81       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      178.32        18.18       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 
       22.29         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        68.25        54.02        17.29        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       133.81        91.56       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        64.64        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       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
      102.90        39.29        59.28       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       54.51       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19       201.80        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
      202.65        28.08        27.72        48.85       357.37        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-A3TV 
      174.84        12.43        26.73        77.88         0.20         0.16 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       64.44        62.79        32.48        39.58         6.67         0.69 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            0.33             0.16 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          314.56           357.37 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          46.900           54.265 
[1] "0.3 - 314.6 (46.9)" "0.2 - 357.4 (54.3)"
[1] "hr=" "1.2"
D37V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  BCLAF1 MUTATED                    8             2
  BCLAF1 WILD-TYPE                 31             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  BCLAF1 MUTATED                                           9
  BCLAF1 WILD-TYPE                                        51
                  vv
clus               REGIONAL LYMPH NODE
  BCLAF1 MUTATED                    29
  BCLAF1 WILD-TYPE                 142
D37V4, multiclass
                                           clus
vv                                          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  DISTANT METASTASIS                                     8               31
  PRIMARY TUMOR                                          2                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              9               51
  REGIONAL LYMPH NODE                                   29              142
[1] 4 2
[1] 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      21        8       22       11
                  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        26         10
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  BCLAF1 MUTATED            4          9        2
  BCLAF1 WILD-TYPE         19         37       14
D37V5, multiclass
             clus
vv            BCLAF1 MUTATED BCLAF1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  3               21
  STAGE IA                 2                8
  STAGE IB                 2               22
  STAGE II                 5               11
  STAGE IIA                3                7
  STAGE IIB                3               11
  STAGE IIC                0                9
  STAGE III                6               26
  STAGE IIIA               3               10
  STAGE IIIB               4               19
  STAGE IIIC               9               37
  STAGE IV                 2               14
[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    45 51 42 47
D37V6, multiclass
       clus
vv      BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T0+T1              7               45
  T2                 8               51
  T3                12               42
  T4                10               47
[1] 4 2
[1] TRUE
[1] "dimension of 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 119  39  27  29
D37V7, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  N0             20              119
  N1              9               39
  N2              6               27
  N3              7               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
  BCLAF1 MUTATED    41   1   0   1   1
  BCLAF1 WILD-TYPE 203   3   3   1   7
D37V8, multiclass
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  M0              41              203
  M1               1                3
  M1A              0                3
  M1B              1                1
  M1C              1                7
[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 87 56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     16   12
  BCLAF1 WILD-TYPE   87   56
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  NO              16               87
  YES             12               56
[1] 2 2
[1] FALSE
D37V10, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    11  37
  BCLAF1 WILD-TYPE  25 202
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     11   37
  BCLAF1 WILD-TYPE   25  202
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  NO              11               25
  YES             37              202
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    13  35
  BCLAF1 WILD-TYPE  93 135
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     13   35
  BCLAF1 WILD-TYPE   93  135
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE             13               93
  MALE               35              135
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED       0                         0    48
  BCLAF1 WILD-TYPE     3                         1   224
D37V13, multiclass
                           clus
vv                          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 48              224
[1] 3 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  48
  BCLAF1 WILD-TYPE   3 221
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      0   48
  BCLAF1 WILD-TYPE    3  221
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             48              221
[1] 2 2
[1] FALSE

Clustering(38) Variable = ZFX MUTATION ANALYSIS
D38V1, survival
               sevent
clus2             0   1
  ZFX MUTATED     7   6
  ZFX WILD-TYPE 119 134
  ZFX MUTATED ZFX WILD-TYPE 
           13           253 
  ZFX MUTATED ZFX WILD-TYPE 
            6           134 
$`ZFX MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17Z TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       44.19        10.03         6.31        34.29        55.69         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        86.76        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       11.57        10.55         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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       35.54        28.31        33.83         5.42        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.81        49.15         8.68         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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 
       10.13        16.24        15.42        12.16        14.70         0.33 
TCGA-RP-A694 
        0.69 

  ZFX MUTATED ZFX WILD-TYPE 
         1.15          0.13 
  ZFX MUTATED ZFX WILD-TYPE 
        63.42        125.65 
  ZFX MUTATED ZFX WILD-TYPE 
        27.39         16.24 
[1] "1.1 - 63.4 (27.4)"  "0.1 - 125.7 (16.2)"
[1] "hr=" "1.2"
D38V2, survival
               sevent
clus2             0   1
  ZFX MUTATED     7   6
  ZFX WILD-TYPE 122 135
  ZFX MUTATED ZFX WILD-TYPE 
           13           257 
  ZFX MUTATED ZFX WILD-TYPE 
            6           135 
$`ZFX MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17Z TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       62.07        20.38         8.65        67.43       126.81        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        86.76        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        59.28       314.56       161.03 
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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         0.33         0.69 

  ZFX MUTATED ZFX WILD-TYPE 
         6.67          0.16 
  ZFX MUTATED ZFX WILD-TYPE 
       126.81        357.37 
  ZFX MUTATED ZFX WILD-TYPE 
        49.48         52.01 
[1] "6.7 - 126.8 (49.5)" "0.2 - 357.4 (52.0)"
[1] "hr=" "1.3"
D38V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  ZFX MUTATED                    3             0
  ZFX WILD-TYPE                 36             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ZFX MUTATED                                           3                   7
  ZFX WILD-TYPE                                        57                 164
D38V4, multiclass
                                           clus
vv                                          ZFX MUTATED ZFX WILD-TYPE
  DISTANT METASTASIS                                  3            36
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           3            57
  REGIONAL LYMPH NODE                                 7           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
  ZFX MUTATED             0       0       0        1        1        2
  ZFX WILD-TYPE          10       6      24        9       23       14
               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        30         13         22
               vv
clus            STAGE IIIC STAGE IV
  ZFX MUTATED            1        1
  ZFX WILD-TYPE         45       15
D38V5, multiclass
             clus
vv            ZFX MUTATED ZFX WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            24
  STAGE IA              1             9
  STAGE IB              1            23
  STAGE II              2            14
  STAGE IIA             1             9
  STAGE IIB             3            11
  STAGE IIC             0             9
  STAGE III             2            30
  STAGE IIIA            0            13
  STAGE IIIB            1            22
  STAGE IIIC            1            45
  STAGE IV              1            15
[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    50 56 50 53
D38V6, multiclass
       clus
vv      ZFX MUTATED ZFX WILD-TYPE
  T0+T1           2            50
  T2              3            56
  T3              4            50
  T4              4            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
  ZFX MUTATED     9   2   0   2
  ZFX WILD-TYPE 130  46  33  34
D38V7, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  N0           9           130
  N1           2            46
  N2           0            33
  N3           2            34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  ZFX MUTATED    12   0   1   0   0
  ZFX WILD-TYPE 232   4   2   2   8
D38V8, multiclass
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  M0           12           232
  M1            0             4
  M1A           1             2
  M1B           0             2
  M1C           0             8
[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 97 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      6    4
  ZFX WILD-TYPE   97   64
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO            6            97
  YES           4            64
[1] 2 2
[1] FALSE
D38V10, binary
               cls
clus              0   1
  ZFX MUTATED     1  12
  ZFX WILD-TYPE  35 227
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      1   12
  ZFX WILD-TYPE   35  227
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO            1            35
  YES          12           227
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, binary
               cls
clus              0   1
  ZFX MUTATED     2  11
  ZFX WILD-TYPE 104 159
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      2   11
  ZFX WILD-TYPE  104  159
        clus
vv       ZFX MUTATED ZFX WILD-TYPE
  FEMALE           2           104
  MALE            11           159
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFX MUTATED       0                         0    13
  ZFX WILD-TYPE     3                         1   259
D38V13, multiclass
                           clus
vv                          ZFX MUTATED ZFX WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              13           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"
D38V14, binary
               cls
clus              0   1
  ZFX MUTATED     1  12
  ZFX WILD-TYPE   2 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      1   12
  ZFX WILD-TYPE    2  257
                        clus
vv                       ZFX MUTATED ZFX WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          12           257
[1] 2 2
[1] FALSE

Clustering(39) Variable = BRAF MUTATION ANALYSIS
D39V1, survival
                sevent
clus2             0  1
  BRAF MUTATED   69 63
  BRAF WILD-TYPE 57 77
  BRAF MUTATED BRAF WILD-TYPE 
           132            134 
  BRAF MUTATED BRAF WILD-TYPE 
            63             77 
$`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        59.57        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        54.74        54.31        21.44 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       25.78        52.01        13.68        17.72        23.11        21.93 
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        60.23 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       15.85         9.21         7.99        37.97        62.79        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 
       39.62         9.50        12.03        32.15        11.31        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM 
       51.12        34.29        60.00        47.21        19.43        28.31 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.69        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       125.65        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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       12.72         3.22        22.92         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       21.73        31.40        38.40        25.18         3.78        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P 
       11.11       114.15        34.88         4.21        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL 
        9.57        36.07        11.80         1.87        12.62         1.71 
TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
        5.62        85.74         3.45        11.01         7.33        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
        8.22        11.08        30.87        47.38         8.81        49.15 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
        5.23        14.20         5.98         0.99         0.16        17.33 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-QB-A6FS 
        7.23         0.85        11.61        44.28        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        86.76        44.19        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        29.23 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D9-A3Z1 
       93.21        31.30        32.28        32.61        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-EB-A5UL 
        7.00        13.15         0.20        23.15        19.00        13.35 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
       11.57         6.31         8.12         1.35         5.13         4.31 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L 
        4.34         1.18         9.90        11.15         8.55         1.08 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        8.09         8.84         9.99         2.43         8.09        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       36.30         9.67        17.98        30.08        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MD 
       33.83         5.42         1.15        36.33        47.51         9.53 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        2.73        14.56        63.42       111.91        56.02        25.08 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AE 
       60.49        53.16        52.67         5.56        51.62        30.15 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 
       21.60        21.60        16.14        22.22        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N 
       12.95         5.72        76.41         3.52        13.45        42.84 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
        6.58        17.72        78.44         1.51        13.08        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW 
        9.04         6.58        22.49        18.41        15.72        64.47 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
       23.80        14.24        15.52         7.30         3.39        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
        7.17        12.92        12.89        52.08         8.65        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-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A3OT 
       10.78         6.41         2.27         0.20         0.13         9.90 
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-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  BRAF MUTATED BRAF WILD-TYPE 
          0.16           0.13 
  BRAF MUTATED BRAF WILD-TYPE 
        125.65         114.67 
  BRAF MUTATED BRAF WILD-TYPE 
         21.52          15.06 
[1] "0.2 - 125.7 (21.5)" "0.1 - 114.7 (15.1)"
[1] "hr=" "1.4"
D39V2, survival
                sevent
clus2             0  1
  BRAF MUTATED   71 64
  BRAF WILD-TYPE 58 77
  BRAF MUTATED BRAF WILD-TYPE 
           135            135 
  BRAF MUTATED BRAF WILD-TYPE 
            64             77 
$`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        59.57        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        55.73       145.12        22.62 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       26.89       135.75       178.32        18.18       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        22.29         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       133.81        91.56       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       47.84        63.78        64.64        56.84        18.61        56.42 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
      195.02        46.82        86.14        59.28        67.43       161.03 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT 
      208.04        89.33        75.48       126.81        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       158.63       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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 
      201.80        27.35        51.35       109.58        31.40        50.76 
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-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC 
        6.44        61.05       162.08        50.89        37.25        43.82 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX 
       23.34        31.27        33.21         6.77       174.21        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.79       357.37        53.52        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FB 
      101.26        11.41       148.80        27.02       174.84        26.73 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       22.92         0.16        19.30         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A265 TCGA-QB-A6FS 
      139.89        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        86.76        62.07       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        45.30 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D9-A149 
      174.84        56.35        32.94        63.81       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        68.25        54.02 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 
       17.29        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        36.82        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-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       47.28       268.73       204.66        96.23       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
       47.54       134.40       162.48        71.21        53.26        51.62 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI 
       54.51        36.95        64.08        34.32        53.19       148.08 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L 
       35.44        13.94         9.17        77.75        12.59       131.51 
TCGA-ER-A19N TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       44.05         8.88       148.18        79.99        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P 
       32.05       247.04        80.32        46.98        92.98        15.72 
TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      216.92       202.65        20.91        28.08        27.72        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       40.27         9.70        47.38        23.93        74.73       133.55 
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-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       28.73        12.43        49.45        77.88         0.20        47.54 
TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        9.90       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       39.58         0.33         0.69 

  BRAF MUTATED BRAF WILD-TYPE 
          0.16           0.20 
  BRAF MUTATED BRAF WILD-TYPE 
        357.37         314.56 
  BRAF MUTATED BRAF WILD-TYPE 
         55.73          48.85 
[1] "0.2 - 357.4 (55.7)" "0.2 - 314.6 (48.9)"
[1] "hr=" "1.4"
D39V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  BRAF MUTATED                   12             2
  BRAF WILD-TYPE                 27             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  BRAF MUTATED                                          28                  97
  BRAF WILD-TYPE                                        32                  74
D39V4, multiclass
                                           clus
vv                                          BRAF MUTATED BRAF WILD-TYPE
  DISTANT METASTASIS                                  12             27
  PRIMARY TUMOR                                        2              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           28             32
  REGIONAL LYMPH NODE                                 97             74
[1] 4 2
[1] 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      14        3       13        8
  BRAF WILD-TYPE           3       4      10        7       11        8
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BRAF MUTATED           4         4         4        22          7         11
  BRAF WILD-TYPE         6        10         5        10          6         12
                vv
clus             STAGE IIIC STAGE IV
  BRAF MUTATED           20        7
  BRAF WILD-TYPE         26        9
D39V5, multiclass
             clus
vv            BRAF MUTATED BRAF WILD-TYPE
  I OR II NOS            7              3
  STAGE 0                2              4
  STAGE I               14             10
  STAGE IA               3              7
  STAGE IB              13             11
  STAGE II               8              8
  STAGE IIA              4              6
  STAGE IIB              4             10
  STAGE IIC              4              5
  STAGE III             22             10
  STAGE IIIA             7              6
  STAGE IIIB            11             12
  STAGE IIIC            20             26
  STAGE IV               7              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
  BRAF MUTATED      33 32 33 17
  BRAF WILD-TYPE    19 27 21 40
D39V6, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  T0+T1           33             19
  T2              32             27
  T3              33             21
  T4              17             40
[1] 4 2
[1] TRUE
[1] "dimension of 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 19 14
  BRAF WILD-TYPE 73 17 14 22
D39V7, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           66             73
  N1           31             17
  N2           19             14
  N3           14             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
  BRAF MUTATED   126   1   2   1   4
  BRAF WILD-TYPE 118   3   1   1   4
D39V8, multiclass
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  M0           126            118
  M1             1              3
  M1A            2              1
  M1B            1              1
  M1C            4              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"
D39V9, binary
                cls
clus              0  1
  BRAF MUTATED   49 31
  BRAF WILD-TYPE 54 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     49   31
  BRAF WILD-TYPE   54   37
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            49             54
  YES           31             37
[1] 2 2
[1] FALSE
D39V10, binary
                cls
clus               0   1
  BRAF MUTATED    20 118
  BRAF WILD-TYPE  16 121
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     20  118
  BRAF WILD-TYPE   16  121
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            20             16
  YES          118            121
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, binary
                cls
clus              0  1
  BRAF MUTATED   56 83
  BRAF WILD-TYPE 50 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     56   83
  BRAF WILD-TYPE   50   87
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           56             50
  MALE             83             87
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       1                         0   138
  BRAF WILD-TYPE     2                         1   134
D39V13, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                              138            134
[1] 3 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     1 136
  BRAF WILD-TYPE   2 133
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1  136
  BRAF WILD-TYPE    2  133
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO          136            133
[1] 2 2
[1] FALSE

Clustering(40) Variable = SAG MUTATION ANALYSIS
D40V1, survival
               sevent
clus2             0   1
  SAG MUTATED     5   4
  SAG WILD-TYPE 121 136
  SAG MUTATED SAG WILD-TYPE 
            9           257 
  SAG MUTATED SAG WILD-TYPE 
            4           136 
$`SAG MUTATED`
TCGA-D9-A6EA TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 
       11.31        39.62         2.43        30.08        55.69         8.84 
TCGA-EE-A2MC TCGA-EE-A2MR TCGA-FS-A1ZZ 
       47.51        60.49         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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        47.21        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-A2MD 
       34.98        36.33        98.27         2.70         6.18         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-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-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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  SAG MUTATED SAG WILD-TYPE 
         2.43          0.13 
  SAG MUTATED SAG WILD-TYPE 
        60.49        125.65 
  SAG MUTATED SAG WILD-TYPE 
        30.08         16.47 
[1] "2.4 - 60.5 (30.1)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.2"
D40V2, survival
               sevent
clus2             0   1
  SAG MUTATED     5   4
  SAG WILD-TYPE 124 137
  SAG MUTATED SAG WILD-TYPE 
            9           261 
  SAG MUTATED SAG WILD-TYPE 
            4           137 
$`SAG MUTATED`
TCGA-D9-A6EA TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 
       25.18        56.84        25.87        48.72       126.81        21.67 
TCGA-EE-A2MC TCGA-EE-A2MR TCGA-FS-A1ZZ 
       61.51       134.40        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03       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-A2MF 
      129.27        28.83        19.76        47.28       103.27       268.73 
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       158.63       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       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  SAG MUTATED SAG WILD-TYPE 
        21.67          0.16 
  SAG MUTATED SAG WILD-TYPE 
       134.40        357.37 
  SAG MUTATED SAG WILD-TYPE 
        48.72         52.01 
[1] "21.7 - 134.4 (48.7)" "0.2 - 357.4 (52.0)" 
[1] "hr=" "1.1"
D40V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  SAG MUTATED                    2             1
  SAG WILD-TYPE                 37             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SAG MUTATED                                           2                   6
  SAG WILD-TYPE                                        58                 165
D40V4, multiclass
                                           clus
vv                                          SAG MUTATED SAG WILD-TYPE
  DISTANT METASTASIS                                  2            37
  PRIMARY TUMOR                                       1             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           2            58
  REGIONAL LYMPH NODE                                 6           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
  SAG MUTATED             1       1       3        1        1        1
  SAG WILD-TYPE           9       5      21        9       23       15
               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        32         13         23
               vv
clus            STAGE IIIC STAGE IV
  SAG MUTATED            2        0
  SAG WILD-TYPE         44       16
D40V5, multiclass
             clus
vv            SAG MUTATED SAG WILD-TYPE
  I OR II NOS           1             9
  STAGE 0               1             5
  STAGE I               3            21
  STAGE IA              1             9
  STAGE IB              1            23
  STAGE II              1            15
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             0             9
  STAGE III             0            32
  STAGE IIIA            0            13
  STAGE IIIB            0            23
  STAGE IIIC            2            44
  STAGE IV              0            16
[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    51 55 51 56
D40V6, multiclass
       clus
vv      SAG MUTATED SAG WILD-TYPE
  T0+T1           1            51
  T2              4            55
  T3              3            51
  T4              1            56
[1] 4 2
[1] TRUE
[1] "dimension of 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 130  47  33  35
D40V7, multiclass
    clus
vv   SAG MUTATED SAG WILD-TYPE
  N0           9           130
  N1           1            47
  N2           0            33
  N3           1            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  SAG MUTATED    11   0   0   0   0
  SAG WILD-TYPE 233   4   3   2   8
D40V8, multiclass
     clus
vv    SAG MUTATED SAG WILD-TYPE
  M0           11           233
  M1            0             4
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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 96 66
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      7    2
  SAG WILD-TYPE   96   66
     clus
vv    SAG MUTATED SAG WILD-TYPE
  NO            7            96
  YES           2            66
[1] 2 2
[1] FALSE
D40V10, binary
               cls
clus              0   1
  SAG MUTATED     0  11
  SAG WILD-TYPE  36 228
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      0   11
  SAG WILD-TYPE   36  228
     clus
vv    SAG MUTATED SAG WILD-TYPE
  NO            0            36
  YES          11           228
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, binary
               cls
clus              0   1
  SAG MUTATED     3   8
  SAG WILD-TYPE 103 162
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      3    8
  SAG WILD-TYPE  103  162
        clus
vv       SAG MUTATED SAG WILD-TYPE
  FEMALE           3           103
  MALE             8           162
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SAG MUTATED       0                         0    11
  SAG WILD-TYPE     3                         1   261
D40V13, multiclass
                           clus
vv                          SAG MUTATED SAG WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              11           261
[1] 3 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   2 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      1   10
  SAG WILD-TYPE    2  259
                        clus
vv                       SAG MUTATED SAG WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          10           259
[1] 2 2
[1] FALSE

Clustering(41) Variable = OR51S1 MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2                0   1
  OR51S1 MUTATED    16  14
  OR51S1 WILD-TYPE 110 126
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              30              236 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              14              126 
$`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        54.31        13.22        12.20 
TCGA-EE-A20C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GI 
        4.34        36.85        39.62         9.50        34.29        30.08 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A2MT 
       55.69         5.42        63.42       125.65        53.16        52.67 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19H TCGA-FS-A1Z3 
       21.60        27.35        18.41        33.60        34.88        14.24 
TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       12.89        28.73         0.99        11.61        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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 
       59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       93.21        54.74        31.30        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       25.78        52.01        47.87        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01        21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.12         1.35         5.13         4.31        60.23 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q 
       11.15        62.79         8.55         1.08        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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       33.83         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM 
        2.73        44.25         7.96        14.56       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        26.99        21.60        60.49         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        0.95        21.73        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-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.11       114.15         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       19.53        11.08         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-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        17.33         9.90         7.23         0.85        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       31.33        84.72        16.24        12.16        14.70         5.79 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  OR51S1 MUTATED OR51S1 WILD-TYPE 
            0.99             0.13 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          125.65           124.31 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          29.405           15.980 
[1] "1.0 - 125.7 (29.4)" "0.1 - 124.3 (16.0)"
[1] "hr=" "1.4"
D41V2, survival
                  sevent
clus2                0   1
  OR51S1 MUTATED    16  14
  OR51S1 WILD-TYPE 113 127
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              30              240 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              14              127 
$`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       145.12        66.25        26.89 
TCGA-EE-A20C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GI 
      151.27        64.64        56.84        18.61        67.43        48.72 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A2MT 
      126.81        13.91        96.23       158.63       162.48        71.21 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19H TCGA-FS-A1Z3 
       36.95        27.35        51.35       148.08       152.35        20.91 
TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       23.93        28.73        22.92        11.74        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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 
       59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
      174.84        55.73        56.35        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       135.75       137.92       178.32        18.18       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        22.29 
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        68.25        54.02        17.29 
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       133.81        91.56       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        63.78 
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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28       314.56       161.03       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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96       204.66       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       134.40        53.26       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JH 
      127.20        64.08        34.32        53.19       201.80       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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-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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       64.44        32.48        39.58         6.67         0.33         0.69 

  OR51S1 MUTATED OR51S1 WILD-TYPE 
           10.13             0.16 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          162.48           357.37 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          54.095           51.815 
[1] "10.1 - 162.5 (54.1)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1"  
D41V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  OR51S1 MUTATED                    4             1
  OR51S1 WILD-TYPE                 35             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  OR51S1 MUTATED                                          10
  OR51S1 WILD-TYPE                                        50
                  vv
clus               REGIONAL LYMPH NODE
  OR51S1 MUTATED                    15
  OR51S1 WILD-TYPE                 156
D41V4, multiclass
                                           clus
vv                                          OR51S1 MUTATED OR51S1 WILD-TYPE
  DISTANT METASTASIS                                     4               35
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               50
  REGIONAL LYMPH NODE                                   15              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
  OR51S1 MUTATED             1       2       1        2        3        3
  OR51S1 WILD-TYPE           9       4      23        8       21       13
                  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        25         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  OR51S1 MUTATED            3          2        1
  OR51S1 WILD-TYPE         20         44       15
D41V5, multiclass
             clus
vv            OR51S1 MUTATED OR51S1 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  1               23
  STAGE IA                 2                8
  STAGE IB                 3               21
  STAGE II                 3               13
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                7               25
  STAGE IIIA               1               12
  STAGE IIIB               3               20
  STAGE IIIC               2               44
  STAGE IV                 1               15
[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    48 55 49 51
D41V6, multiclass
       clus
vv      OR51S1 MUTATED OR51S1 WILD-TYPE
  T0+T1              4               48
  T2                 4               55
  T3                 5               49
  T4                 6               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
  OR51S1 MUTATED    18   6   2   2
  OR51S1 WILD-TYPE 121  42  31  34
D41V7, multiclass
    clus
vv   OR51S1 MUTATED OR51S1 WILD-TYPE
  N0             18              121
  N1              6               42
  N2              2               31
  N3              2               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  OR51S1 MUTATED    27   1   0   0   0
  OR51S1 WILD-TYPE 217   3   3   2   8
D41V8, multiclass
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  M0              27              217
  M1               1                3
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 90 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     13    4
  OR51S1 WILD-TYPE   90   64
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  NO              13               90
  YES              4               64
[1] 2 2
[1] FALSE
D41V10, binary
                  cls
clus                 0   1
  OR51S1 MUTATED     6  24
  OR51S1 WILD-TYPE  30 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED      6   24
  OR51S1 WILD-TYPE   30  215
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  NO               6               30
  YES             24              215
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, binary
                  cls
clus                 0   1
  OR51S1 MUTATED    11  19
  OR51S1 WILD-TYPE  95 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     11   19
  OR51S1 WILD-TYPE   95  151
        clus
vv       OR51S1 MUTATED OR51S1 WILD-TYPE
  FEMALE             11               95
  MALE               19              151
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR51S1 MUTATED       0                         0    30
  OR51S1 WILD-TYPE     3                         1   242
D41V13, multiclass
                           clus
vv                          OR51S1 MUTATED OR51S1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 30              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"
D41V14, binary
                  cls
clus                 0   1
  OR51S1 MUTATED     0  30
  OR51S1 WILD-TYPE   3 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED      0   30
  OR51S1 WILD-TYPE    3  239
                        clus
vv                       OR51S1 MUTATED OR51S1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             30              239
[1] 2 2
[1] FALSE

Clustering(42) Variable = USP17L2 MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  USP17L2 MUTATED    11  10
  USP17L2 WILD-TYPE 115 130
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               21               245 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               10               130 
$`USP17L2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-EE-A181 
       70.16        44.19        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 
       60.23        39.62        36.30        30.08        63.42        60.49 
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        86.76        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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01        21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        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-A20C 
        8.12         1.35        12.20         5.13         4.31         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         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        32.15 
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        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
       26.99        21.60        53.16        52.67       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       51.62         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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        18.41        21.73        33.60        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       20.38        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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
        7.36        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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  USP17L2 MUTATED USP17L2 WILD-TYPE 
             0.99              0.13 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
            82.29            125.65 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
            28.73             16.47 
[1] "1.0 - 82.3 (28.7)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.2"
D42V2, survival
                   sevent
clus2                 0   1
  USP17L2 MUTATED    11  10
  USP17L2 WILD-TYPE 118 131
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               21               249 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               10               131 
$`USP17L2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-EE-A181 
       71.80        62.07       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 
      133.81        56.84        36.82        48.72        96.23       134.40 
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        86.76        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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25        54.02        17.29 
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        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         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       195.02        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        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       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 
      162.48        71.21       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        23.47       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      109.58       148.08        35.44        13.94        50.76        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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-A1ZE 
       28.08         7.79        27.72        48.85       357.37        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-A4F8 
       49.48        27.09        27.02        77.82        66.67       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  USP17L2 MUTATED USP17L2 WILD-TYPE 
             9.17              0.16 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
           166.52            357.37 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
            53.26             51.62 
[1] "9.2 - 166.5 (53.3)" "0.2 - 357.4 (51.6)"
[1] "hr=" "1.1"
D42V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  USP17L2 MUTATED                    2             1
  USP17L2 WILD-TYPE                 37             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  USP17L2 MUTATED                                           6
  USP17L2 WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  USP17L2 MUTATED                    13
  USP17L2 WILD-TYPE                 158
D42V4, multiclass
                                           clus
vv                                          USP17L2 MUTATED USP17L2 WILD-TYPE
  DISTANT METASTASIS                                      2                37
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                54
  REGIONAL LYMPH NODE                                    13               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
  USP17L2 MUTATED             1       0       1        3        2        3
  USP17L2 WILD-TYPE           9       6      23        7       22       13
                   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        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  USP17L2 MUTATED            0          4        1
  USP17L2 WILD-TYPE         23         42       15
D42V5, multiclass
             clus
vv            USP17L2 MUTATED USP17L2 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   1                23
  STAGE IA                  3                 7
  STAGE IB                  2                22
  STAGE II                  3                13
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 0                 9
  STAGE III                 3                29
  STAGE IIIA                1                12
  STAGE IIIB                0                23
  STAGE IIIC                4                42
  STAGE IV                  1                15
[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    49 54 48 52
D42V6, multiclass
       clus
vv      USP17L2 MUTATED USP17L2 WILD-TYPE
  T0+T1               3                49
  T2                  5                54
  T3                  6                48
  T4                  5                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
  USP17L2 MUTATED    13   3   2   2
  USP17L2 WILD-TYPE 126  45  31  34
D42V7, multiclass
    clus
vv   USP17L2 MUTATED USP17L2 WILD-TYPE
  N0              13               126
  N1               3                45
  N2               2                31
  N3               2                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  USP17L2 MUTATED    20   0   0   0   1
  USP17L2 WILD-TYPE 224   4   3   2   7
D42V8, multiclass
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  M0               20               224
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               1                 7
[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 93 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED     10    5
  USP17L2 WILD-TYPE   93   63
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  NO               10                93
  YES               5                63
[1] 2 2
[1] FALSE
D42V10, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     1  21
  USP17L2 WILD-TYPE  35 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      1   21
  USP17L2 WILD-TYPE   35  218
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  NO                1                35
  YES              21               218
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     6  16
  USP17L2 WILD-TYPE 100 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      6   16
  USP17L2 WILD-TYPE  100  154
        clus
vv       USP17L2 MUTATED USP17L2 WILD-TYPE
  FEMALE               6               100
  MALE                16               154
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP17L2 MUTATED       0                         0    22
  USP17L2 WILD-TYPE     3                         1   250
D42V13, multiclass
                           clus
vv                          USP17L2 MUTATED USP17L2 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  22               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"
D42V14, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     0  22
  USP17L2 WILD-TYPE   3 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      0   22
  USP17L2 WILD-TYPE    3  247
                        clus
vv                       USP17L2 MUTATED USP17L2 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              22               247
[1] 2 2
[1] FALSE

Clustering(43) Variable = LRPPRC MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  LRPPRC MUTATED     6   9
  LRPPRC WILD-TYPE 120 131
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              15              251 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
               9              131 
$`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        62.79         1.08 
TCGA-EE-A2GC TCGA-EE-A2GS TCGA-EE-A2MS TCGA-EE-A3AA TCGA-ER-A193 TCGA-ER-A19F 
       34.29        13.02        53.16       124.31        31.40        11.11 
TCGA-ER-A19M TCGA-FS-A1ZD TCGA-GF-A6C9 
       28.60         8.22        11.61 

$`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        86.76        11.41        44.19 
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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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-A20I 
        5.13         4.31        60.23         4.34        15.85         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        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        36.33        51.12        17.98        60.00        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-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       55.69         5.42         1.15        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       21.73        33.60        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-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        13.45        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-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        17.33         9.90         7.23         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  LRPPRC MUTATED LRPPRC WILD-TYPE 
            1.08             0.13 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
          124.31           125.65 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
           28.60            16.47 
[1] "1.1 - 124.3 (28.6)" "0.1 - 125.7 (16.5)"
[1] "hr=" "1.1"
D43V2, survival
                  sevent
clus2                0   1
  LRPPRC MUTATED     6   9
  LRPPRC WILD-TYPE 123 132
  LRPPRC MUTATED LRPPRC WILD-TYPE 
              15              255 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
               9              132 
$`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        63.78         2.60 
TCGA-EE-A2GC TCGA-EE-A2GS TCGA-EE-A2MS TCGA-EE-A3AA TCGA-ER-A193 TCGA-ER-A19F 
       67.43        55.59       162.48       124.31        31.40        26.37 
TCGA-ER-A19M TCGA-FS-A1ZD TCGA-GF-A6C9 
       61.05        53.52        11.74 

$`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        86.76        11.87        62.07 
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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56        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        64.64        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       134.40        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        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 
       19.30         9.90         7.23         2.04       139.89       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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  LRPPRC MUTATED LRPPRC WILD-TYPE 
            2.60             0.16 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
          168.26           357.37 
  LRPPRC MUTATED LRPPRC WILD-TYPE 
           61.05            50.76 
[1] "2.6 - 168.3 (61.0)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1.2"
D43V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  LRPPRC MUTATED                    2             0
  LRPPRC WILD-TYPE                 37             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  LRPPRC MUTATED                                           3
  LRPPRC WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  LRPPRC MUTATED                    10
  LRPPRC WILD-TYPE                 161
D43V4, multiclass
                                           clus
vv                                          LRPPRC MUTATED LRPPRC WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              3               57
  REGIONAL LYMPH NODE                                   10              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
  LRPPRC MUTATED             0       0       1        0        2        1
  LRPPRC WILD-TYPE          10       6      23       10       22       15
                  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        29         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  LRPPRC MUTATED            2          2        0
  LRPPRC WILD-TYPE         21         44       16
D43V5, multiclass
             clus
vv            LRPPRC MUTATED LRPPRC WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 0               10
  STAGE IB                 2               22
  STAGE II                 1               15
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                3               29
  STAGE IIIA               0               13
  STAGE IIIB               2               21
  STAGE IIIC               2               44
  STAGE IV                 0               16
[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    50 55 50 55
D43V6, multiclass
       clus
vv      LRPPRC MUTATED LRPPRC WILD-TYPE
  T0+T1              2               50
  T2                 4               55
  T3                 4               50
  T4                 2               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
  LRPPRC MUTATED     8   3   1   2
  LRPPRC WILD-TYPE 131  45  32  34
D43V7, multiclass
    clus
vv   LRPPRC MUTATED LRPPRC WILD-TYPE
  N0              8              131
  N1              3               45
  N2              1               32
  N3              2               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  LRPPRC MUTATED    14   0   0   0   0
  LRPPRC WILD-TYPE 230   4   3   2   8
D43V8, multiclass
     clus
vv    LRPPRC MUTATED LRPPRC WILD-TYPE
  M0              14              230
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 98 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      5    4
  LRPPRC WILD-TYPE   98   64
     clus
vv    LRPPRC MUTATED LRPPRC WILD-TYPE
  NO               5               98
  YES              4               64
[1] 2 2
[1] FALSE
D43V10, binary
                  cls
clus                 0   1
  LRPPRC MUTATED     3  12
  LRPPRC WILD-TYPE  33 227
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      3   12
  LRPPRC WILD-TYPE   33  227
     clus
vv    LRPPRC MUTATED LRPPRC WILD-TYPE
  NO               3               33
  YES             12              227
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, binary
                  cls
clus                 0   1
  LRPPRC MUTATED     3  12
  LRPPRC WILD-TYPE 103 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      3   12
  LRPPRC WILD-TYPE  103  158
        clus
vv       LRPPRC MUTATED LRPPRC WILD-TYPE
  FEMALE              3              103
  MALE               12              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRPPRC MUTATED       0                         0    15
  LRPPRC WILD-TYPE     3                         1   257
D43V13, multiclass
                           clus
vv                          LRPPRC MUTATED LRPPRC WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 15              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"
D43V14, binary
                  cls
clus                 0   1
  LRPPRC MUTATED     0  15
  LRPPRC WILD-TYPE   3 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRPPRC MUTATED      0   15
  LRPPRC WILD-TYPE    3  254
                        clus
vv                       LRPPRC MUTATED LRPPRC WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             15              254
[1] 2 2
[1] FALSE

Clustering(44) Variable = BTK MUTATION ANALYSIS
D44V1, survival
               sevent
clus2             0   1
  BTK MUTATED    11   4
  BTK WILD-TYPE 115 136
  BTK MUTATED BTK WILD-TYPE 
           15           251 
  BTK MUTATED BTK WILD-TYPE 
            4           136 
$`BTK MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51T TCGA-DA-A1HV 
       44.19        56.19        64.44       103.59        25.78        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        60.49        30.15        34.88 
TCGA-ER-A1A1 TCGA-FS-A1Z3 TCGA-GF-A6C9 
       78.44        14.24        11.61 

$`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        86.76        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        59.57       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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87        13.68        17.72        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 
       21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34        15.85 
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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
        5.56       124.31       122.73        51.62         3.68        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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-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        17.33         9.90         7.23         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  BTK MUTATED BTK WILD-TYPE 
         1.12          0.13 
  BTK MUTATED BTK WILD-TYPE 
       103.59        125.65 
  BTK MUTATED BTK WILD-TYPE 
        44.19         15.95 
[1] "1.1 - 103.6 (44.2)" "0.1 - 125.7 (15.9)"
[1] "hr=" "3"  
D44V2, survival
               sevent
clus2             0   1
  BTK MUTATED    12   4
  BTK WILD-TYPE 117 137
  BTK MUTATED BTK WILD-TYPE 
           16           254 
  BTK MUTATED BTK WILD-TYPE 
            4           137 
$`BTK MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51T TCGA-D9-A149 
       62.07        56.19        66.08       103.59        26.89        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       134.40        54.51 
TCGA-ER-A19H TCGA-ER-A1A1 TCGA-FS-A1Z3 TCGA-GF-A6C9 
      152.35        79.99        20.91        11.74 

$`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        86.76        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        59.57       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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       203.05       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       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  BTK MUTATED BTK WILD-TYPE 
        11.74          0.16 
  BTK MUTATED BTK WILD-TYPE 
       152.35        357.37 
  BTK MUTATED BTK WILD-TYPE 
       59.130        50.825 
[1] "11.7 - 152.3 (59.1)" "0.2 - 357.4 (50.8)" 
[1] "hr=" "2.1"
D44V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  BTK MUTATED                    3             0
  BTK WILD-TYPE                 36             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  BTK MUTATED                                           5                   8
  BTK WILD-TYPE                                        55                 163
D44V4, multiclass
                                           clus
vv                                          BTK MUTATED BTK WILD-TYPE
  DISTANT METASTASIS                                  3            36
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           5            55
  REGIONAL LYMPH NODE                                 8           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
  BTK MUTATED             0       0       1        2        0        1
  BTK WILD-TYPE          10       6      23        8       24       15
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BTK MUTATED           0         0         1         2          0          2
  BTK WILD-TYPE        10        14         8        30         13         21
               vv
clus            STAGE IIIC STAGE IV
  BTK MUTATED            4        1
  BTK WILD-TYPE         42       15
D44V5, multiclass
             clus
vv            BTK MUTATED BTK WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               1            23
  STAGE IA              2             8
  STAGE IB              0            24
  STAGE II              1            15
  STAGE IIA             0            10
  STAGE IIB             0            14
  STAGE IIC             1             8
  STAGE III             2            30
  STAGE IIIA            0            13
  STAGE IIIB            2            21
  STAGE IIIC            4            42
  STAGE IV              1            15
[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    47 57 53 55
D44V6, multiclass
       clus
vv      BTK MUTATED BTK WILD-TYPE
  T0+T1           5            47
  T2              2            57
  T3              1            53
  T4              2            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
  BTK MUTATED     7   4   1   3
  BTK WILD-TYPE 132  44  32  33
D44V7, multiclass
    clus
vv   BTK MUTATED BTK WILD-TYPE
  N0           7           132
  N1           4            44
  N2           1            32
  N3           3            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
  BTK MUTATED    14   1   0   0   0
  BTK WILD-TYPE 230   3   3   2   8
D44V8, multiclass
     clus
vv    BTK MUTATED BTK WILD-TYPE
  M0           14           230
  M1            1             3
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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 99 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      4    4
  BTK WILD-TYPE   99   64
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO            4            99
  YES           4            64
[1] 2 2
[1] FALSE
D44V10, binary
               cls
clus              0   1
  BTK MUTATED     6  10
  BTK WILD-TYPE  30 229
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      6   10
  BTK WILD-TYPE   30  229
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO            6            30
  YES          10           229
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, binary
               cls
clus              0   1
  BTK MUTATED     9   7
  BTK WILD-TYPE  97 163
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      9    7
  BTK WILD-TYPE   97  163
        clus
vv       BTK MUTATED BTK WILD-TYPE
  FEMALE           9            97
  MALE             7           163
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTK MUTATED       0                         0    16
  BTK WILD-TYPE     3                         1   256
D44V13, multiclass
                           clus
vv                          BTK MUTATED BTK WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              16           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"
D44V14, binary
               cls
clus              0   1
  BTK MUTATED     0  16
  BTK WILD-TYPE   3 253
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      0   16
  BTK WILD-TYPE    3  253
                        clus
vv                       BTK MUTATED BTK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          16           253
[1] 2 2
[1] FALSE

Clustering(45) Variable = DSG3 MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  DSG3 MUTATED    21  25
  DSG3 WILD-TYPE 105 115
  DSG3 MUTATED DSG3 WILD-TYPE 
            46            220 
  DSG3 MUTATED DSG3 WILD-TYPE 
            25            115 
$`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-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29E 
       13.35         1.12         1.35        12.20         9.21        62.79 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GN 
        1.08         8.84         9.67        34.29        19.43        33.83 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ 
       55.69         1.15        98.27        47.51        14.56        63.42 
TCGA-EE-A2MR TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A19G TCGA-ER-A19N 
       60.49        13.81        21.60        27.35       114.15        42.84 
TCGA-ER-A19P TCGA-ER-A19S TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
       34.68        36.07        14.24        12.89         8.65         5.23 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A266 
        6.41         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        86.76        11.41        44.19 
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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
       17.72        23.11         4.01        21.93        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        23.15        19.00 
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        60.23         4.34        15.85         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        36.85        39.62 
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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        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-A2MF TCGA-EE-A2MG 
        2.70         6.18         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96       125.65       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        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        30.15        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       22.92        21.60        16.14        22.22         0.95        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q 
       11.11        34.88         4.21        13.45        28.60         9.57 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        47.38        52.08         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-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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  DSG3 MUTATED DSG3 WILD-TYPE 
          0.99           0.13 
  DSG3 MUTATED DSG3 WILD-TYPE 
        114.15         125.65 
  DSG3 MUTATED DSG3 WILD-TYPE 
        14.400         17.445 
[1] "1.0 - 114.2 (14.4)" "0.1 - 125.7 (17.4)"
[1] "hr=" "1"  
D45V2, survival
                sevent
clus2              0   1
  DSG3 MUTATED    21  25
  DSG3 WILD-TYPE 108 116
  DSG3 MUTATED DSG3 WILD-TYPE 
            46            224 
  DSG3 MUTATED DSG3 WILD-TYPE 
            25            116 
$`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 
       17.29        33.73        14.70        26.89       168.26        63.78 
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 
      126.81        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 
      134.40        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        86.76        11.87        62.07 
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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29        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        68.25        54.02        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        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        64.64        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        36.82        86.14        59.28       314.56       161.03 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       47.28       103.27       268.73       103.20        16.96       158.63 
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       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       54.51        23.47       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       109.58       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-A19Q TCGA-ER-A19T TCGA-ER-A19W 
        6.44       131.51        61.05        50.89         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        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-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-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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       12.43        26.73         0.20        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  DSG3 MUTATED DSG3 WILD-TYPE 
          2.60           0.16 
  DSG3 MUTATED DSG3 WILD-TYPE 
        268.93         357.37 
  DSG3 MUTATED DSG3 WILD-TYPE 
        47.935         53.175 
[1] "2.6 - 268.9 (47.9)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.1"
D45V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  DSG3 MUTATED                    8             1
  DSG3 WILD-TYPE                 31             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DSG3 MUTATED                                          11                  27
  DSG3 WILD-TYPE                                        49                 144
D45V4, multiclass
                                           clus
vv                                          DSG3 MUTATED DSG3 WILD-TYPE
  DISTANT METASTASIS                                   8             31
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           11             49
  REGIONAL LYMPH NODE                                 27            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
  DSG3 MUTATED             1       1       4        1        1        4
  DSG3 WILD-TYPE           9       5      20        9       23       12
                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        26         11         18
                vv
clus             STAGE IIIC STAGE IV
  DSG3 MUTATED            8        4
  DSG3 WILD-TYPE         38       12
D45V5, multiclass
             clus
vv            DSG3 MUTATED DSG3 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                4             20
  STAGE IA               1              9
  STAGE IB               1             23
  STAGE II               4             12
  STAGE IIA              2              8
  STAGE IIB              3             11
  STAGE IIC              0              9
  STAGE III              6             26
  STAGE IIIA             2             11
  STAGE IIIB             5             18
  STAGE IIIC             8             38
  STAGE IV               4             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
  DSG3 MUTATED       8  8  9  9
  DSG3 WILD-TYPE    44 51 45 48
D45V6, multiclass
       clus
vv      DSG3 MUTATED DSG3 WILD-TYPE
  T0+T1            8             44
  T2               8             51
  T3               9             45
  T4               9             48
[1] 4 2
[1] TRUE
[1] "dimension of 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 117  39  27  30
D45V7, multiclass
    clus
vv   DSG3 MUTATED DSG3 WILD-TYPE
  N0           22            117
  N1            9             39
  N2            6             27
  N3            6             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
  DSG3 MUTATED    40   1   1   0   2
  DSG3 WILD-TYPE 204   3   2   2   6
D45V8, multiclass
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  M0            40            204
  M1             1              3
  M1A            1              2
  M1B            0              2
  M1C            2              6
[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 87 58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     16   10
  DSG3 WILD-TYPE   87   58
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO            16             87
  YES           10             58
[1] 2 2
[1] FALSE
D45V10, binary
                cls
clus               0   1
  DSG3 MUTATED     9  38
  DSG3 WILD-TYPE  27 201
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      9   38
  DSG3 WILD-TYPE   27  201
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO             9             27
  YES           38            201
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, binary
                cls
clus               0   1
  DSG3 MUTATED    17  30
  DSG3 WILD-TYPE  89 140
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     17   30
  DSG3 WILD-TYPE   89  140
        clus
vv       DSG3 MUTATED DSG3 WILD-TYPE
  FEMALE           17             89
  MALE             30            140
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSG3 MUTATED       1                         0    46
  DSG3 WILD-TYPE     2                         1   226
D45V13, multiclass
                           clus
vv                          DSG3 MUTATED DSG3 WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               46            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"
D45V14, binary
                cls
clus               0   1
  DSG3 MUTATED     1  46
  DSG3 WILD-TYPE   2 223
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      1   46
  DSG3 WILD-TYPE    2  223
                        clus
vv                       DSG3 MUTATED DSG3 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           46            223
[1] 2 2
[1] FALSE

Clustering(46) Variable = C1QTNF9 MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  C1QTNF9 MUTATED    10   6
  C1QTNF9 WILD-TYPE 116 134
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               250 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                6               134 
$`C1QTNF9 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A51N TCGA-D9-A3Z1 TCGA-EE-A29A TCGA-EE-A29M 
       81.24        44.19        21.44         4.01         7.99        39.62 
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        60.49         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        86.76        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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       23.11        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        62.79         8.55        36.85 
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-A2A2 TCGA-EE-A2A5 
        2.43        32.15         8.09        11.31        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        33.83        55.69 
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-A2MF 
       98.27         2.70         6.18        47.51        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       25.08        26.99        21.60        53.16        52.67       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       12.72        22.92        21.60        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A4FB 
        5.23        53.85         7.36        28.73        14.20         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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
             3.22              0.13 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            81.24            125.65 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           21.520            16.355 
[1] "3.2 - 81.2 (21.5)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1.4"
D46V2, survival
                   sevent
clus2                 0   1
  C1QTNF9 MUTATED    10   6
  C1QTNF9 WILD-TYPE 119 135
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               254 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                6               135 
$`C1QTNF9 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A51N TCGA-D9-A3Z1 TCGA-EE-A29A TCGA-EE-A29M 
       95.74        62.07        22.62        11.34        63.35        56.84 
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       134.40        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        86.76        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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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        22.29 
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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56       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        63.78        72.07        64.64         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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        54.51        13.81        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        34.32       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73       174.84        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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            11.34              0.16 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           204.66            357.37 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            62.71             50.12 
[1] "11.3 - 204.7 (62.7)" "0.2 - 357.4 (50.1)" 
[1] "hr=" "1.6"
D46V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  C1QTNF9 MUTATED                    2             0
  C1QTNF9 WILD-TYPE                 37             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C1QTNF9 MUTATED                                           4
  C1QTNF9 WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  C1QTNF9 MUTATED                    10
  C1QTNF9 WILD-TYPE                 161
D46V4, multiclass
                                           clus
vv                                          C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  DISTANT METASTASIS                                      2                37
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                56
  REGIONAL LYMPH NODE                                    10               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
  C1QTNF9 MUTATED             0       0       2        2        4        1
  C1QTNF9 WILD-TYPE          10       6      22        8       20       15
                   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        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C1QTNF9 MUTATED            0          2        1
  C1QTNF9 WILD-TYPE         23         44       15
D46V5, multiclass
             clus
vv            C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   2                22
  STAGE IA                  2                 8
  STAGE IB                  4                20
  STAGE II                  1                15
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 1                 8
  STAGE III                 1                31
  STAGE IIIA                1                12
  STAGE IIIB                0                23
  STAGE IIIC                2                44
  STAGE IV                  1                15
[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    48 52 52 54
D46V6, multiclass
       clus
vv      C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  T0+T1               4                48
  T2                  7                52
  T3                  2                52
  T4                  3                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
  C1QTNF9 MUTATED    11   1   1   3
  C1QTNF9 WILD-TYPE 128  47  32  33
D46V7, multiclass
    clus
vv   C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  N0              11               128
  N1               1                47
  N2               1                32
  N3               3                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
  C1QTNF9 MUTATED    15   0   0   0   1
  C1QTNF9 WILD-TYPE 229   4   3   2   7
D46V8, multiclass
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  M0               15               229
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               1                 7
[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 96 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      7    4
  C1QTNF9 WILD-TYPE   96   64
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  NO                7                96
  YES               4                64
[1] 2 2
[1] FALSE
D46V10, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     2  14
  C1QTNF9 WILD-TYPE  34 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      2   14
  C1QTNF9 WILD-TYPE   34  225
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  NO                2                34
  YES              14               225
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     4  12
  C1QTNF9 WILD-TYPE 102 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      4   12
  C1QTNF9 WILD-TYPE  102  158
        clus
vv       C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  FEMALE               4               102
  MALE                12               158
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QTNF9 MUTATED       0                         0    16
  C1QTNF9 WILD-TYPE     3                         1   256
D46V13, multiclass
                           clus
vv                          C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               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"
D46V14, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     0  15
  C1QTNF9 WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      0   15
  C1QTNF9 WILD-TYPE    3  254
                        clus
vv                       C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               254
[1] 2 2
[1] FALSE

Clustering(47) Variable = BLM MUTATION ANALYSIS
D47V1, survival
               sevent
clus2             0   1
  BLM MUTATED     9   6
  BLM WILD-TYPE 117 134
  BLM MUTATED BLM WILD-TYPE 
           15           251 
  BLM MUTATED BLM WILD-TYPE 
            6           134 
$`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 
       62.79        34.29         9.53       124.31        11.11         1.71 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A262 
       10.78         0.99        44.28 

$`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        86.76        11.41        44.19         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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87        13.68        17.72        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
       21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        17.98        60.00        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        55.69 
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-A2MF 
       98.27         2.70         6.18        47.51        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       11.61        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  BLM MUTATED BLM WILD-TYPE 
         0.99          0.13 
  BLM MUTATED BLM WILD-TYPE 
       124.31        125.65 
  BLM MUTATED BLM WILD-TYPE 
        13.32         17.33 
[1] "1.0 - 124.3 (13.3)" "0.1 - 125.7 (17.3)"
[1] "hr=" "1.4"
D47V2, survival
               sevent
clus2             0   1
  BLM MUTATED     9   6
  BLM WILD-TYPE 120 135
  BLM MUTATED BLM WILD-TYPE 
           15           255 
  BLM MUTATED BLM WILD-TYPE 
            6           135 
$`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 
       63.78        67.43        47.28       124.31        26.37        33.21 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A262 
       12.43        22.92       139.89 

$`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        86.76        11.87        62.07       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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98         6.77        92.98       174.21        15.72       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-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-GF-A6C9 TCGA-GN-A264 
       19.30         9.90         7.23         2.04        11.74       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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  BLM MUTATED BLM WILD-TYPE 
        12.43          0.16 
  BLM MUTATED BLM WILD-TYPE 
       139.89        357.37 
  BLM MUTATED BLM WILD-TYPE 
        46.98         53.16 
[1] "12.4 - 139.9 (47.0)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1"  
D47V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  BLM MUTATED                    0             0
  BLM WILD-TYPE                 39             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  BLM MUTATED                                           2                  13
  BLM WILD-TYPE                                        58                 158
D47V4, multiclass
                                           clus
vv                                          BLM MUTATED BLM WILD-TYPE
  DISTANT METASTASIS                                  0            39
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           2            58
  REGIONAL LYMPH NODE                                13           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
  BLM MUTATED             0       0       0        0        1        1
  BLM WILD-TYPE          10       6      24       10       23       15
               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        28         13         21
               vv
clus            STAGE IIIC STAGE IV
  BLM MUTATED            1        1
  BLM WILD-TYPE         45       15
D47V5, multiclass
             clus
vv            BLM MUTATED BLM WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            24
  STAGE IA              0            10
  STAGE IB              1            23
  STAGE II              1            15
  STAGE IIA             0            10
  STAGE IIB             2            12
  STAGE IIC             1             8
  STAGE III             4            28
  STAGE IIIA            0            13
  STAGE IIIB            2            21
  STAGE IIIC            1            45
  STAGE IV              1            15
[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    48 58 49 55
D47V6, multiclass
       clus
vv      BLM MUTATED BLM WILD-TYPE
  T0+T1           4            48
  T2              1            58
  T3              5            49
  T4              2            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
  BLM MUTATED     7   4   2   1
  BLM WILD-TYPE 132  44  31  35
D47V7, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  N0           7           132
  N1           4            44
  N2           2            31
  N3           1            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             M0  M1 M1A M1B M1C
  BLM MUTATED    13   0   1   0   0
  BLM WILD-TYPE 231   4   2   2   8
D47V8, multiclass
     clus
vv    BLM MUTATED BLM WILD-TYPE
  M0           13           231
  M1            0             4
  M1A           1             2
  M1B           0             2
  M1C           0             8
[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 100  62
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      3    6
  BLM WILD-TYPE  100   62
     clus
vv    BLM MUTATED BLM WILD-TYPE
  NO            3           100
  YES           6            62
[1] 2 2
[1] FALSE
D47V10, binary
               cls
clus              0   1
  BLM MUTATED     3  12
  BLM WILD-TYPE  33 227
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      3   12
  BLM WILD-TYPE   33  227
     clus
vv    BLM MUTATED BLM WILD-TYPE
  NO            3            33
  YES          12           227
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, binary
               cls
clus              0   1
  BLM MUTATED     4  11
  BLM WILD-TYPE 102 159
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      4   11
  BLM WILD-TYPE  102  159
        clus
vv       BLM MUTATED BLM WILD-TYPE
  FEMALE           4           102
  MALE            11           159
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BLM MUTATED       0                         0    15
  BLM WILD-TYPE     3                         1   257
D47V13, multiclass
                           clus
vv                          BLM MUTATED BLM WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              15           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"
D47V14, binary
               cls
clus              0   1
  BLM MUTATED     0  15
  BLM WILD-TYPE   3 254
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED      0   15
  BLM WILD-TYPE    3  254
                        clus
vv                       BLM MUTATED BLM WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          15           254
[1] 2 2
[1] FALSE

Clustering(48) Variable = ACSM2B MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2                0   1
  ACSM2B MUTATED    20  23
  ACSM2B WILD-TYPE 106 117
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              43              223 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              23              117 
$`ACSM2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D9-A6EA TCGA-D9-A6EC 
       44.19        59.57         6.31       103.59        11.31        13.22 
TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A 
       13.35         1.35        12.20         4.34         9.21         7.99 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V 
       37.97        11.15        62.79         1.08        39.62         2.43 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MF 
       34.29        30.08        28.31        34.98         8.84         2.73 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A3AD TCGA-EE-A3AG 
       44.25        14.56        63.42        56.02         3.68        15.95 
TCGA-EE-A3JD TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A1ZQ 
       27.35        28.60        34.68        78.44        18.41         8.65 
TCGA-FS-A1ZR TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-QB-A6FS 
        8.81        10.78         0.99        84.72        16.24         5.79 
TCGA-RP-A693 
        0.33 

$`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        86.76        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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       25.78        52.01        47.87        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        4.01        21.93         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        23.15        19.00 
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        60.23        15.85         1.18         9.90 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55        36.85         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        36.33        51.12        17.98        60.00        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        55.69         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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73        51.62        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22         0.95        18.41        21.73        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-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        4.21        13.45        42.84         9.57        36.07         6.58 
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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.89        47.38        52.08        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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       14.20         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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       44.28        31.33        10.13        15.42        12.16        14.70 
TCGA-RP-A694 
        0.69 

  ACSM2B MUTATED ACSM2B WILD-TYPE 
            0.33             0.13 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
          103.59           125.65 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
           14.56            17.72 
[1] "0.3 - 103.6 (14.6)" "0.1 - 125.7 (17.7)"
[1] "hr=" "1.1"
D48V2, survival
                  sevent
clus2                0   1
  ACSM2B MUTATED    21  23
  ACSM2B WILD-TYPE 108 118
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              44              226 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
              23              118 
$`ACSM2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D9-A1JW TCGA-D9-A6EA 
       62.07        59.57        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        17.29        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        63.78         2.60        56.84 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A3AD 
      268.73       103.20       204.66        96.23       167.90         3.68 
TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A1A1 TCGA-FR-A3YN 
       23.47        27.35        61.05       162.08        79.99        92.98 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 
      133.55        11.41        12.43        22.92        84.72        64.44 
TCGA-QB-A6FS TCGA-RP-A693 
        6.67         0.33 

$`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        86.76        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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        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       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       91.56        13.55        80.61        72.07        64.64        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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       158.63       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 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19N 
       26.37       268.93       152.35         6.44       131.51        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21         6.77       174.21        15.72       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-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-A4FB TCGA-FS-A4FC 
       77.82        66.67        28.73       174.84        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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        7.23         2.04        11.74       139.89       117.93        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A694 
       62.79        32.48        39.58         0.69 

  ACSM2B MUTATED ACSM2B WILD-TYPE 
            0.33             0.16 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
          268.73           357.37 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
          58.205           51.485 
[1] "0.3 - 268.7 (58.2)" "0.2 - 357.4 (51.5)"
[1] "hr=" "1.1"
D48V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ACSM2B MUTATED                    8             2
  ACSM2B WILD-TYPE                 31             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ACSM2B MUTATED                                           4
  ACSM2B WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  ACSM2B MUTATED                    30
  ACSM2B WILD-TYPE                 141
D48V4, multiclass
                                           clus
vv                                          ACSM2B MUTATED ACSM2B WILD-TYPE
  DISTANT METASTASIS                                     8               31
  PRIMARY TUMOR                                          2                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              4               56
  REGIONAL LYMPH NODE                                   30              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       5        2        4        1
  ACSM2B WILD-TYPE           9       4      19        8       20       15
                  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        25          9
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ACSM2B MUTATED            1          9        1
  ACSM2B WILD-TYPE         22         37       15
D48V5, multiclass
             clus
vv            ACSM2B MUTATED ACSM2B WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  5               19
  STAGE IA                 2                8
  STAGE IB                 4               20
  STAGE II                 1               15
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                1                8
  STAGE III                7               25
  STAGE IIIA               4                9
  STAGE IIIB               1               22
  STAGE IIIC               9               37
  STAGE IV                 1               15
[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 10  8  8
  ACSM2B WILD-TYPE    44 49 46 49
D48V6, multiclass
       clus
vv      ACSM2B MUTATED ACSM2B WILD-TYPE
  T0+T1              8               44
  T2                10               49
  T3                 8               46
  T4                 8               49
[1] 4 2
[1] TRUE
[1] "dimension of 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    21  10   5   6
  ACSM2B WILD-TYPE 118  38  28  30
D48V7, multiclass
    clus
vv   ACSM2B MUTATED ACSM2B WILD-TYPE
  N0             21              118
  N1             10               38
  N2              5               28
  N3              6               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
  ACSM2B MUTATED    42   0   0   0   1
  ACSM2B WILD-TYPE 202   4   3   2   7
D48V8, multiclass
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  M0              42              202
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 87 61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED     16    7
  ACSM2B WILD-TYPE   87   61
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  NO              16               87
  YES              7               61
[1] 2 2
[1] FALSE
D48V10, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     9  35
  ACSM2B WILD-TYPE  27 204
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      9   35
  ACSM2B WILD-TYPE   27  204
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  NO               9               27
  YES             35              204
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, binary
                  cls
clus                 0   1
  ACSM2B MUTATED     7  37
  ACSM2B WILD-TYPE  99 133
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      7   37
  ACSM2B WILD-TYPE   99  133
        clus
vv       ACSM2B MUTATED ACSM2B WILD-TYPE
  FEMALE              7               99
  MALE               37              133
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSM2B MUTATED       0                         0    44
  ACSM2B WILD-TYPE     3                         1   228
D48V13, multiclass
                           clus
vv                          ACSM2B MUTATED ACSM2B WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 44              228
[1] 3 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  43
  ACSM2B WILD-TYPE   3 226
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      0   43
  ACSM2B WILD-TYPE    3  226
                        clus
vv                       ACSM2B MUTATED ACSM2B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             43              226
[1] 2 2
[1] FALSE

Clustering(49) Variable = PARM1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  PARM1 MUTATED     6  13
  PARM1 WILD-TYPE 120 127
  PARM1 MUTATED PARM1 WILD-TYPE 
             19             247 
  PARM1 MUTATED PARM1 WILD-TYPE 
             13             127 
$`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-GF-A6C9 
        7.30        20.38        47.38        52.08         0.99        11.61 
TCGA-GN-A266 
       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        86.76        11.41        44.19         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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       60.23         4.34        15.85         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        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W 
       39.62         9.50         8.09         8.84         9.99        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       51.12        34.29        17.98        60.00        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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22         0.95        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       15.52         7.33         3.39         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        12.92        12.89         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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  PARM1 MUTATED PARM1 WILD-TYPE 
           0.99            0.13 
  PARM1 MUTATED PARM1 WILD-TYPE 
          70.16          125.65 
  PARM1 MUTATED PARM1 WILD-TYPE 
          11.80           17.56 
[1] "1.0 - 70.2 (11.8)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.6"
D49V2, survival
                 sevent
clus2               0   1
  PARM1 MUTATED     6  13
  PARM1 WILD-TYPE 123 128
  PARM1 MUTATED PARM1 WILD-TYPE 
             19             251 
  PARM1 MUTATED PARM1 WILD-TYPE 
             13             128 
$`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-GF-A6C9 
       27.72       357.37       101.26        74.73        22.92        11.74 
TCGA-GN-A266 
       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        86.76        11.87        62.07       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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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 
       63.78        72.07        64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19       201.80        51.35       109.58        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        23.93       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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  PARM1 MUTATED PARM1 WILD-TYPE 
           4.96            0.16 
  PARM1 MUTATED PARM1 WILD-TYPE 
         357.37          314.56 
  PARM1 MUTATED PARM1 WILD-TYPE 
          43.82           53.19 
[1] "5.0 - 357.4 (43.8)" "0.2 - 314.6 (53.2)"
[1] "hr=" "1.4"
D49V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PARM1 MUTATED                    6             0
  PARM1 WILD-TYPE                 33             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PARM1 MUTATED                                           4                   9
  PARM1 WILD-TYPE                                        56                 162
D49V4, multiclass
                                           clus
vv                                          PARM1 MUTATED PARM1 WILD-TYPE
  DISTANT METASTASIS                                    6              33
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              56
  REGIONAL LYMPH NODE                                   9             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
  PARM1 MUTATED             1       0       1        1        2        1
  PARM1 WILD-TYPE           9       6      23        9       22       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PARM1 MUTATED           0         0         1         4          0          2
  PARM1 WILD-TYPE        10        14         8        28         13         21
                 vv
clus              STAGE IIIC STAGE IV
  PARM1 MUTATED            5        0
  PARM1 WILD-TYPE         41       16
D49V5, multiclass
             clus
vv            PARM1 MUTATED PARM1 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                1               9
  STAGE IB                2              22
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               4              28
  STAGE IIIA              0              13
  STAGE IIIB              2              21
  STAGE IIIC              5              41
  STAGE IV                0              16
[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    51 55 51 52
D49V6, multiclass
       clus
vv      PARM1 MUTATED PARM1 WILD-TYPE
  T0+T1             1              51
  T2                4              55
  T3                3              51
  T4                5              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
  PARM1 MUTATED     7   4   4   2
  PARM1 WILD-TYPE 132  44  29  34
D49V7, multiclass
    clus
vv   PARM1 MUTATED PARM1 WILD-TYPE
  N0             7             132
  N1             4              44
  N2             4              29
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  PARM1 MUTATED    17   0   0   0   0
  PARM1 WILD-TYPE 227   4   3   2   8
D49V8, multiclass
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  M0             17             227
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 99 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      4    6
  PARM1 WILD-TYPE   99   62
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  NO              4              99
  YES             6              62
[1] 2 2
[1] FALSE
D49V10, binary
                 cls
clus                0   1
  PARM1 MUTATED     3  16
  PARM1 WILD-TYPE  33 223
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      3   16
  PARM1 WILD-TYPE   33  223
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  NO              3              33
  YES            16             223
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, binary
                 cls
clus                0   1
  PARM1 MUTATED     5  14
  PARM1 WILD-TYPE 101 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      5   14
  PARM1 WILD-TYPE  101  156
        clus
vv       PARM1 MUTATED PARM1 WILD-TYPE
  FEMALE             5             101
  MALE              14             156
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARM1 MUTATED       0                         0    19
  PARM1 WILD-TYPE     3                         1   253
D49V13, multiclass
                           clus
vv                          PARM1 MUTATED PARM1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                19             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"
D49V14, binary
                 cls
clus                0   1
  PARM1 MUTATED     0  19
  PARM1 WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      0   19
  PARM1 WILD-TYPE    3  250
                        clus
vv                       PARM1 MUTATED PARM1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            19             250
[1] 2 2
[1] FALSE

Clustering(50) Variable = TP63 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  TP63 MUTATED    25  22
  TP63 WILD-TYPE 101 118
  TP63 MUTATED TP63 WILD-TYPE 
            47            219 
  TP63 MUTATED TP63 WILD-TYPE 
            22            118 
$`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        32.61        25.78 
TCGA-D3-A5GO TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A29C 
       47.87        21.93        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 
       62.79        36.85        39.62         9.50         8.84        51.12 
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       125.65       111.91        60.49        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-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-RP-A694 
        0.85        11.61        10.13        16.24         0.69 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         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 
       59.57       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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       54.74        31.30        54.31        32.28        21.44        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
       13.68        17.72        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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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 
       60.23         4.34        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q 
        9.90        11.15         8.55         1.08        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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.30         9.67        36.33        17.98        60.00        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 
       55.69         5.42        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        29.46         2.73        44.25         7.96 
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        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         3.68        30.15 
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-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       22.22         0.95        18.41        21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       14.24        15.52         3.39        20.38         8.22        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-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-A3TV TCGA-FW-A5DY 
        5.98         6.41         2.27         0.20         0.16        17.33 
TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
        9.90        44.28        31.33        84.72        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       14.70         5.79         0.33 

  TP63 MUTATED TP63 WILD-TYPE 
          0.13           0.16 
  TP63 MUTATED TP63 WILD-TYPE 
        125.65         124.31 
  TP63 MUTATED TP63 WILD-TYPE 
         16.24          17.33 
[1] "0.1 - 125.7 (16.2)" "0.2 - 124.3 (17.3)"
[1] "hr=" "1.1"
D50V2, survival
                sevent
clus2              0   1
  TP63 MUTATED    25  22
  TP63 WILD-TYPE 104 119
  TP63 MUTATED TP63 WILD-TYPE 
            47            223 
  TP63 MUTATED TP63 WILD-TYPE 
            22            119 
$`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        63.81        26.89 
TCGA-D3-A5GO TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A29C 
      137.92        22.29        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 
       63.78        64.64        56.84        18.61        14.47        59.28 
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       158.63       203.05       134.40        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-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-RP-A694 
        2.04        11.74        10.13        64.44         0.69 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       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 
       59.57       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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN 
       55.73        56.35       145.12        32.94        22.62       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       91.56       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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MM TCGA-EE-A2MN 
      103.27       268.73       103.20        16.96       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       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         3.68        54.51        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18       127.20        36.95        64.08        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       51.35       109.58        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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21         6.77       174.21        15.72 
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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        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-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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
       77.88         0.20         0.16        19.30         9.90       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
      117.93        84.72        62.79        32.48        39.58         6.67 
TCGA-RP-A693 
        0.33 

  TP63 MUTATED TP63 WILD-TYPE 
          0.69           0.16 
  TP63 MUTATED TP63 WILD-TYPE 
        204.66         357.37 
  TP63 MUTATED TP63 WILD-TYPE 
         39.75          54.02 
[1] "0.7 - 204.7 (39.8)" "0.2 - 357.4 (54.0)"
[1] "hr=" "1.2"
D50V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TP63 MUTATED                    7             1
  TP63 WILD-TYPE                 32             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TP63 MUTATED                                           4                  36
  TP63 WILD-TYPE                                        56                 135
D50V4, multiclass
                                           clus
vv                                          TP63 MUTATED TP63 WILD-TYPE
  DISTANT METASTASIS                                   7             32
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             56
  REGIONAL LYMPH NODE                                 36            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
  TP63 MUTATED             1       1       4        1        3        5
  TP63 WILD-TYPE           9       5      20        9       21       11
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TP63 MUTATED           1         5         1         5          5          6
  TP63 WILD-TYPE         9         9         8        27          8         17
                vv
clus             STAGE IIIC STAGE IV
  TP63 MUTATED            6        1
  TP63 WILD-TYPE         40       15
D50V5, multiclass
             clus
vv            TP63 MUTATED TP63 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                4             20
  STAGE IA               1              9
  STAGE IB               3             21
  STAGE II               5             11
  STAGE IIA              1              9
  STAGE IIB              5              9
  STAGE IIC              1              8
  STAGE III              5             27
  STAGE IIIA             5              8
  STAGE IIIB             6             17
  STAGE IIIC             6             40
  STAGE IV               1             15
[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       5  8 14 12
  TP63 WILD-TYPE    47 51 40 45
D50V6, multiclass
       clus
vv      TP63 MUTATED TP63 WILD-TYPE
  T0+T1            5             47
  T2               8             51
  T3              14             40
  T4              12             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
  TP63 MUTATED    24  10   7   2
  TP63 WILD-TYPE 115  38  26  34
D50V7, multiclass
    clus
vv   TP63 MUTATED TP63 WILD-TYPE
  N0           24            115
  N1           10             38
  N2            7             26
  N3            2             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  TP63 MUTATED    44   0   0   0   1
  TP63 WILD-TYPE 200   4   3   2   7
D50V8, multiclass
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  M0            44            200
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            1              7
[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 83 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     20   11
  TP63 WILD-TYPE   83   57
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO            20             83
  YES           11             57
[1] 2 2
[1] FALSE
D50V10, binary
                cls
clus               0   1
  TP63 MUTATED     8  40
  TP63 WILD-TYPE  28 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      8   40
  TP63 WILD-TYPE   28  199
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO             8             28
  YES           40            199
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, binary
                cls
clus               0   1
  TP63 MUTATED    16  32
  TP63 WILD-TYPE  90 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     16   32
  TP63 WILD-TYPE   90  138
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  FEMALE           16             90
  MALE             32            138
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP63 MUTATED       0                         0    48
  TP63 WILD-TYPE     3                         1   224
D50V13, multiclass
                           clus
vv                          TP63 MUTATED TP63 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               48            224
[1] 3 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  47
  TP63 WILD-TYPE   2 222
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      1   47
  TP63 WILD-TYPE    2  222
                        clus
vv                       TP63 MUTATED TP63 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           47            222
[1] 2 2
[1] FALSE

Clustering(51) Variable = NGF MUTATION ANALYSIS
D51V1, survival
               sevent
clus2             0   1
  NGF MUTATED     5   4
  NGF WILD-TYPE 121 136
  NGF MUTATED NGF WILD-TYPE 
            9           257 
  NGF MUTATED NGF WILD-TYPE 
            4           136 
$`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 
       53.16         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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       32.28        21.44        32.61        25.78        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        19.00        13.35        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 
       60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  NGF MUTATED NGF WILD-TYPE 
         5.23          0.13 
  NGF MUTATED NGF WILD-TYPE 
       110.79        125.65 
  NGF MUTATED NGF WILD-TYPE 
        13.22         17.33 
[1] "5.2 - 110.8 (13.2)" "0.1 - 125.7 (17.3)"
[1] "hr=" "1.3"
D51V2, survival
               sevent
clus2             0   1
  NGF MUTATED     5   4
  NGF WILD-TYPE 124 137
  NGF MUTATED NGF WILD-TYPE 
            9           261 
  NGF MUTATED NGF WILD-TYPE 
            4           137 
$`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 
      162.48        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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62        63.81        26.89       178.32        18.18 
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 
       22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       17.29        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        63.78        72.07        64.64         2.60        56.84 
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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  NGF MUTATED NGF WILD-TYPE 
        10.13          0.16 
  NGF MUTATED NGF WILD-TYPE 
       162.48        357.37 
  NGF MUTATED NGF WILD-TYPE 
        55.92         51.35 
[1] "10.1 - 162.5 (55.9)" "0.2 - 357.4 (51.4)" 
[1] "hr=" "1.2"
D51V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NGF MUTATED                    3             0
  NGF WILD-TYPE                 36             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NGF MUTATED                                           1                   5
  NGF WILD-TYPE                                        59                 166
D51V4, multiclass
                                           clus
vv                                          NGF MUTATED NGF WILD-TYPE
  DISTANT METASTASIS                                  3            36
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           1            59
  REGIONAL LYMPH NODE                                 5           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
  NGF MUTATED             0       0       1        0        1        2
  NGF WILD-TYPE          10       6      23       10       23       14
               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        32         13         22
               vv
clus            STAGE IIIC STAGE IV
  NGF MUTATED            0        0
  NGF WILD-TYPE         46       16
D51V5, multiclass
             clus
vv            NGF MUTATED NGF WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               1            23
  STAGE IA              0            10
  STAGE IB              1            23
  STAGE II              2            14
  STAGE IIA             1             9
  STAGE IIB             1            13
  STAGE IIC             1             8
  STAGE III             0            32
  STAGE IIIA            0            13
  STAGE IIIB            1            22
  STAGE IIIC            0            46
  STAGE IV              0            16
[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    49 59 51 55
D51V6, multiclass
       clus
vv      NGF MUTATED NGF WILD-TYPE
  T0+T1           3            49
  T2              0            59
  T3              3            51
  T4              2            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
  NGF MUTATED     6   0   1   0
  NGF WILD-TYPE 133  48  32  36
D51V7, multiclass
    clus
vv   NGF MUTATED NGF WILD-TYPE
  N0           6           133
  N1           0            48
  N2           1            32
  N3           0            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             M0  M1 M1A M1B M1C
  NGF MUTATED     8   0   0   0   0
  NGF WILD-TYPE 236   4   3   2   8
D51V8, multiclass
     clus
vv    NGF MUTATED NGF WILD-TYPE
  M0            8           236
  M1            0             4
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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 100  66
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    2
  NGF WILD-TYPE  100   66
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            3           100
  YES           2            66
[1] 2 2
[1] FALSE
D51V10, binary
               cls
clus              0   1
  NGF MUTATED     2   7
  NGF WILD-TYPE  34 232
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      2    7
  NGF WILD-TYPE   34  232
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            2            34
  YES           7           232
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, binary
               cls
clus              0   1
  NGF MUTATED     3   6
  NGF WILD-TYPE 103 164
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    6
  NGF WILD-TYPE  103  164
        clus
vv       NGF MUTATED NGF WILD-TYPE
  FEMALE           3           103
  MALE             6           164
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NGF MUTATED       0                         0     9
  NGF WILD-TYPE     3                         1   263
D51V13, multiclass
                           clus
vv                          NGF MUTATED NGF WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               9           263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
               cls
clus              0   1
  NGF MUTATED     1   8
  NGF WILD-TYPE   2 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      1    8
  NGF WILD-TYPE    2  261
                        clus
vv                       NGF MUTATED NGF WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO           8           261
[1] 2 2
[1] FALSE

Clustering(52) Variable = ANO4 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  ANO4 MUTATED    19  24
  ANO4 WILD-TYPE 107 116
  ANO4 MUTATED ANO4 WILD-TYPE 
            43            223 
  ANO4 MUTATED ANO4 WILD-TYPE 
            24            116 
$`ANO4 MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51R 
      111.09        85.32        44.19         6.31       103.59        32.61 
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        62.79         1.08        39.62         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-A2MF TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC 
        2.73         7.96       111.91        60.49        53.16        51.62 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A195 TCGA-FS-A1ZD 
       30.15        15.95        21.60        27.35        18.61         8.22 
TCGA-FS-A1ZZ TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-QB-A6FS 
        5.23         5.98         0.99         0.13        11.61         5.79 
TCGA-RP-A694 
        0.69 

$`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        86.76        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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN 
       31.30        54.31        32.28        21.44        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        19.00        13.35        13.22        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        60.23 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W 
        8.55        36.85        12.03         8.84         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       51.12        34.29        17.98        60.00        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       35.54        28.31        33.83        55.69         5.42        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        9.53        29.46        44.25        14.56        63.42       125.65 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
       56.02        25.08        26.99        21.60        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31       122.73         3.68        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       22.92        21.60        16.14        22.22         0.95        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       21.73        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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-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-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       14.20        10.78         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 
       17.33         9.90         7.23         0.85        44.28        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-RP-A693 
        0.33 

  ANO4 MUTATED ANO4 WILD-TYPE 
          0.13           0.16 
  ANO4 MUTATED ANO4 WILD-TYPE 
        111.91         125.65 
  ANO4 MUTATED ANO4 WILD-TYPE 
         11.61          17.72 
[1] "0.1 - 111.9 (11.6)" "0.2 - 125.7 (17.7)"
[1] "hr=" "1.2"
D52V2, survival
                sevent
clus2              0   1
  ANO4 MUTATED    19  24
  ANO4 WILD-TYPE 110 117
  ANO4 MUTATED ANO4 WILD-TYPE 
            43            227 
  ANO4 MUTATED ANO4 WILD-TYPE 
            24            117 
$`ANO4 MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51R 
      112.04       103.10        62.07        13.87       103.59        63.81 
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        63.78         2.60        56.84        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-A2MF TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC 
      268.73        16.96       203.05       134.40       162.48        51.62 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A195 TCGA-FS-A1ZD 
       54.51        23.47        36.95        27.35        35.44        53.52 
TCGA-FS-A1ZZ TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-QB-A6FS 
       27.02        26.73        22.92        47.54        11.74         6.67 
TCGA-RP-A694 
        0.69 

$`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        86.76        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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN 
       56.35       145.12        32.94        22.62        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       17.29        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       133.81        91.56       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        64.64 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       56.42        14.47        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      314.56       161.03        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       126.81        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       158.63       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        71.21        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45        77.88         0.20         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         2.04       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 
       64.44        62.79        32.48        39.58         0.33 

  ANO4 MUTATED ANO4 WILD-TYPE 
          0.69           0.16 
  ANO4 MUTATED ANO4 WILD-TYPE 
        268.73         357.37 
  ANO4 MUTATED ANO4 WILD-TYPE 
         48.72          53.16 
[1] "0.7 - 268.7 (48.7)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.1"
D52V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  ANO4 MUTATED                    7             0
  ANO4 WILD-TYPE                 32             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ANO4 MUTATED                                           7                  30
  ANO4 WILD-TYPE                                        53                 141
D52V4, multiclass
                                           clus
vv                                          ANO4 MUTATED ANO4 WILD-TYPE
  DISTANT METASTASIS                                   7             32
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            7             53
  REGIONAL LYMPH NODE                                 30            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       4        4        1        4
  ANO4 WILD-TYPE           8       5      20        6       23       12
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ANO4 MUTATED           3         2         0         8          1          3
  ANO4 WILD-TYPE         7        12         9        24         12         20
                vv
clus             STAGE IIIC STAGE IV
  ANO4 MUTATED            8        1
  ANO4 WILD-TYPE         38       15
D52V5, multiclass
             clus
vv            ANO4 MUTATED ANO4 WILD-TYPE
  I OR II NOS            2              8
  STAGE 0                1              5
  STAGE I                4             20
  STAGE IA               4              6
  STAGE IB               1             23
  STAGE II               4             12
  STAGE IIA              3              7
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              8             24
  STAGE IIIA             1             12
  STAGE IIIB             3             20
  STAGE IIIC             8             38
  STAGE IV               1             15
[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 10 12  5
  ANO4 WILD-TYPE    43 49 42 52
D52V6, multiclass
       clus
vv      ANO4 MUTATED ANO4 WILD-TYPE
  T0+T1            9             43
  T2              10             49
  T3              12             42
  T4               5             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
  ANO4 MUTATED    23   7   6   5
  ANO4 WILD-TYPE 116  41  27  31
D52V7, multiclass
    clus
vv   ANO4 MUTATED ANO4 WILD-TYPE
  N0           23            116
  N1            7             41
  N2            6             27
  N3            5             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
  ANO4 MUTATED    41   0   0   0   1
  ANO4 WILD-TYPE 203   4   3   2   7
D52V8, multiclass
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  M0            41            203
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            1              7
[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 87 59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     16    9
  ANO4 WILD-TYPE   87   59
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  NO            16             87
  YES            9             59
[1] 2 2
[1] FALSE
D52V10, binary
                cls
clus               0   1
  ANO4 MUTATED     7  37
  ANO4 WILD-TYPE  29 202
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED      7   37
  ANO4 WILD-TYPE   29  202
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  NO             7             29
  YES           37            202
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, binary
                cls
clus               0   1
  ANO4 MUTATED    11  33
  ANO4 WILD-TYPE  95 137
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     11   33
  ANO4 WILD-TYPE   95  137
        clus
vv       ANO4 MUTATED ANO4 WILD-TYPE
  FEMALE           11             95
  MALE             33            137
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANO4 MUTATED       0                         0    44
  ANO4 WILD-TYPE     3                         1   228
D52V13, multiclass
                           clus
vv                          ANO4 MUTATED ANO4 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               44            228
[1] 3 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  42
  ANO4 WILD-TYPE   2 227
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED      1   42
  ANO4 WILD-TYPE    2  227
                        clus
vv                       ANO4 MUTATED ANO4 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           42            227
[1] 2 2
[1] FALSE

Clustering(53) Variable = PCDH18 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  PCDH18 MUTATED    22  27
  PCDH18 WILD-TYPE 104 113
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              49              217 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              27              113 
$`PCDH18 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3CB TCGA-D3-A51F TCGA-D9-A6EC 
       81.24        44.19        36.16        82.29        54.74        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        39.62         9.99        49.22 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MF 
       51.12        34.29         1.15        13.02         8.84         2.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3JA 
       14.56        63.42       111.91       124.31       122.73        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19D 
        0.95        27.35        33.60        31.40        76.41         3.52 
TCGA-ER-A19E TCGA-ER-A19N TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZK 
       11.90        42.84        11.74         1.71        23.80        12.89 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       27.39         5.23         0.99        11.61        10.13        15.42 
TCGA-QB-A6FS 
        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        86.76        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        59.57       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        29.23        93.21 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87        13.68        17.72        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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-A20F TCGA-EE-A20I TCGA-EE-A29A 
        5.13         4.31        60.23        15.85         1.18         7.99 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       37.97        62.79        36.85         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
        8.84         2.43        32.15         8.09        11.31        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        9.67        36.33        17.98        60.00        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        55.69 
TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        5.42        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-A2MK 
       47.51         9.53        29.46        44.25         7.96       125.65 
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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       52.67         5.56        51.62         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-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       16.14        18.41        21.73        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        5.72        25.18         3.78        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       13.08        12.62         9.04         6.58        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-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-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-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        17.33         9.90         7.23         0.85        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 
       31.33        84.72        16.24        12.16        14.70         0.33 
TCGA-RP-A694 
        0.69 

  PCDH18 MUTATED PCDH18 WILD-TYPE 
            0.95             0.13 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
          124.31           125.65 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
           13.22            17.72 
[1] "0.9 - 124.3 (13.2)" "0.1 - 125.7 (17.7)"
[1] "hr=" "1.1"
D53V2, survival
                  sevent
clus2                0   1
  PCDH18 MUTATED    22  27
  PCDH18 WILD-TYPE 107 114
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              49              221 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
              27              114 
$`PCDH18 MUTATED`
TCGA-D3-A1QB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3CB TCGA-D3-A51F TCGA-D9-A6EC 
       95.74        62.07        42.08       166.52        55.73        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        56.84        55.92       102.90 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MF 
       59.28        67.43        14.30        55.59        21.67       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3JA 
      204.66        96.23       203.05       124.31       122.73        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19A TCGA-ER-A19D 
      201.80        27.35       148.08        31.40        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19N TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZK 
       13.02        44.05        32.05        33.21       202.65        23.93 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       49.48        27.02        22.92        11.74        10.13        62.79 
TCGA-QB-A6FS 
        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        86.76        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        59.57       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        45.30       174.84 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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 
      133.81        91.56        13.55        63.35        47.84        63.78 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       64.64        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 
      195.02        17.92        46.82        36.82        39.29        86.14 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
      109.58        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-A19T TCGA-ER-A19W 
       61.05       162.08        50.89        37.25         8.88       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-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.72       216.92        48.59       228.59        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-A1ZY 
      133.55        11.41       148.80        53.16        26.56        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-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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       64.44        32.48        39.58         0.33         0.69 

  PCDH18 MUTATED PCDH18 WILD-TYPE 
            2.60             0.16 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
          268.73           357.37 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
           55.92            50.76 
[1] "2.6 - 268.7 (55.9)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1"  
D53V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PCDH18 MUTATED                    9             1
  PCDH18 WILD-TYPE                 30             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PCDH18 MUTATED                                          10
  PCDH18 WILD-TYPE                                        50
                  vv
clus               REGIONAL LYMPH NODE
  PCDH18 MUTATED                    30
  PCDH18 WILD-TYPE                 141
D53V4, multiclass
                                           clus
vv                                          PCDH18 MUTATED PCDH18 WILD-TYPE
  DISTANT METASTASIS                                     9               30
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               50
  REGIONAL LYMPH NODE                                   30              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
  PCDH18 MUTATED             1       2       4        2        7        4
  PCDH18 WILD-TYPE           9       4      20        8       17       12
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PCDH18 MUTATED           1         6         0         7          2
  PCDH18 WILD-TYPE         9         8         9        25         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PCDH18 MUTATED            3          7        2
  PCDH18 WILD-TYPE         20         39       14
D53V5, multiclass
             clus
vv            PCDH18 MUTATED PCDH18 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  4               20
  STAGE IA                 2                8
  STAGE IB                 7               17
  STAGE II                 4               12
  STAGE IIA                1                9
  STAGE IIB                6                8
  STAGE IIC                0                9
  STAGE III                7               25
  STAGE IIIA               2               11
  STAGE IIIB               3               20
  STAGE IIIC               7               39
  STAGE IV                 2               14
[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 14 11 10
  PCDH18 WILD-TYPE    45 45 43 47
D53V6, multiclass
       clus
vv      PCDH18 MUTATED PCDH18 WILD-TYPE
  T0+T1              7               45
  T2                14               45
  T3                11               43
  T4                10               47
[1] 4 2
[1] TRUE
[1] "dimension of 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    30   7   6   4
  PCDH18 WILD-TYPE 109  41  27  32
D53V7, multiclass
    clus
vv   PCDH18 MUTATED PCDH18 WILD-TYPE
  N0             30              109
  N1              7               41
  N2              6               27
  N3              4               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
  PCDH18 MUTATED    45   1   1   0   0
  PCDH18 WILD-TYPE 199   3   2   2   8
D53V8, multiclass
     clus
vv    PCDH18 MUTATED PCDH18 WILD-TYPE
  M0              45              199
  M1               1                3
  M1A              1                2
  M1B              0                2
  M1C              0                8
[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 84 57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED     19   11
  PCDH18 WILD-TYPE   84   57
     clus
vv    PCDH18 MUTATED PCDH18 WILD-TYPE
  NO              19               84
  YES             11               57
[1] 2 2
[1] FALSE
D53V10, binary
                  cls
clus                 0   1
  PCDH18 MUTATED     9  41
  PCDH18 WILD-TYPE  27 198
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED      9   41
  PCDH18 WILD-TYPE   27  198
     clus
vv    PCDH18 MUTATED PCDH18 WILD-TYPE
  NO               9               27
  YES             41              198
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, binary
                  cls
clus                 0   1
  PCDH18 MUTATED    13  37
  PCDH18 WILD-TYPE  93 133
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED     13   37
  PCDH18 WILD-TYPE   93  133
        clus
vv       PCDH18 MUTATED PCDH18 WILD-TYPE
  FEMALE             13               93
  MALE               37              133
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCDH18 MUTATED       0                         0    50
  PCDH18 WILD-TYPE     3                         1   222
D53V13, multiclass
                           clus
vv                          PCDH18 MUTATED PCDH18 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 50              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"
D53V14, binary
                  cls
clus                 0   1
  PCDH18 MUTATED     1  49
  PCDH18 WILD-TYPE   2 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED      1   49
  PCDH18 WILD-TYPE    2  220
                        clus
vv                       PCDH18 MUTATED PCDH18 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             49              220
[1] 2 2
[1] FALSE

Clustering(54) Variable = NMS MUTATION ANALYSIS
D54V1, survival
               sevent
clus2             0   1
  NMS MUTATED     8   5
  NMS WILD-TYPE 118 135
  NMS MUTATED NMS WILD-TYPE 
           13           253 
  NMS MUTATED NMS WILD-TYPE 
            5           135 
$`NMS MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-EE-A181 TCGA-EE-A29S TCGA-EE-A29V 
       44.19        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        86.76        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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       47.21        19.43        16.01        35.54        33.83        55.69 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67         5.56       122.73        51.62         3.68 
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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-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-A4EO 
        0.20         0.99         0.13         0.16        17.33         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  NMS MUTATED NMS WILD-TYPE 
         1.12          0.13 
  NMS MUTATED NMS WILD-TYPE 
       124.31        125.65 
  NMS MUTATED NMS WILD-TYPE 
        28.31         16.24 
[1] "1.1 - 124.3 (28.3)" "0.1 - 125.7 (16.2)"
[1] "hr=" "1.6"
D54V2, survival
               sevent
clus2             0   1
  NMS MUTATED     8   5
  NMS WILD-TYPE 121 136
  NMS MUTATED NMS WILD-TYPE 
           13           257 
  NMS MUTATED NMS WILD-TYPE 
            5           136 
$`NMS MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-EE-A181 TCGA-EE-A29S TCGA-EE-A29V 
       62.07        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        86.76        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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
       56.84        18.61        56.42        37.35        14.47       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       59.28        67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       122.73        51.62         3.68        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19       201.80        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       47.54         0.16        19.30         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  NMS MUTATED NMS WILD-TYPE 
         9.90          0.16 
  NMS MUTATED NMS WILD-TYPE 
       124.31        357.37 
  NMS MUTATED NMS WILD-TYPE 
        48.72         52.01 
[1] "9.9 - 124.3 (48.7)" "0.2 - 357.4 (52.0)"
[1] "hr=" "1"  
D54V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  NMS MUTATED                    3             0
  NMS WILD-TYPE                 36             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NMS MUTATED                                           3                   7
  NMS WILD-TYPE                                        57                 164
D54V4, multiclass
                                           clus
vv                                          NMS MUTATED NMS WILD-TYPE
  DISTANT METASTASIS                                  3            36
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           3            57
  REGIONAL LYMPH NODE                                 7           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
  NMS MUTATED             0       0       0        3        0        1
  NMS WILD-TYPE          10       6      24        7       24       15
               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        30         13         23
               vv
clus            STAGE IIIC STAGE IV
  NMS MUTATED            4        1
  NMS WILD-TYPE         42       15
D54V5, multiclass
             clus
vv            NMS MUTATED NMS WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            24
  STAGE IA              3             7
  STAGE IB              0            24
  STAGE II              1            15
  STAGE IIA             1             9
  STAGE IIB             0            14
  STAGE IIC             1             8
  STAGE III             2            30
  STAGE IIIA            0            13
  STAGE IIIB            0            23
  STAGE IIIC            4            42
  STAGE IV              1            15
[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    48 59 50 56
D54V6, multiclass
       clus
vv      NMS MUTATED NMS WILD-TYPE
  T0+T1           4            48
  T2              0            59
  T3              4            50
  T4              1            56
[1] 4 2
[1] TRUE
[1] "dimension of 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   1   2   3
  NMS WILD-TYPE 132  47  31  33
D54V7, multiclass
    clus
vv   NMS MUTATED NMS WILD-TYPE
  N0           7           132
  N1           1            47
  N2           2            31
  N3           3            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
  NMS MUTATED    12   1   0   0   0
  NMS WILD-TYPE 232   3   3   2   8
D54V8, multiclass
     clus
vv    NMS MUTATED NMS WILD-TYPE
  M0           12           232
  M1            1             3
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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 99 65
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      4    3
  NMS WILD-TYPE   99   65
     clus
vv    NMS MUTATED NMS WILD-TYPE
  NO            4            99
  YES           3            65
[1] 2 2
[1] FALSE
D54V10, binary
               cls
clus              0   1
  NMS MUTATED     3  10
  NMS WILD-TYPE  33 229
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      3   10
  NMS WILD-TYPE   33  229
     clus
vv    NMS MUTATED NMS WILD-TYPE
  NO            3            33
  YES          10           229
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, binary
               cls
clus              0   1
  NMS MUTATED     7   6
  NMS WILD-TYPE  99 164
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      7    6
  NMS WILD-TYPE   99  164
        clus
vv       NMS MUTATED NMS WILD-TYPE
  FEMALE           7            99
  MALE             6           164
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NMS MUTATED       0                         0    13
  NMS WILD-TYPE     3                         1   259
D54V13, multiclass
                           clus
vv                          NMS MUTATED NMS WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              13           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"
D54V14, binary
               cls
clus              0   1
  NMS MUTATED     0  13
  NMS WILD-TYPE   3 256
[1] "tbl2"
               cls
clus            [,1] [,2]
  NMS MUTATED      0   13
  NMS WILD-TYPE    3  256
                        clus
vv                       NMS MUTATED NMS WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          13           256
[1] 2 2
[1] FALSE

Clustering(55) Variable = C12ORF43 MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  C12ORF43 MUTATED     2   3
  C12ORF43 WILD-TYPE 124 137
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                261 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 3                137 
$`C12ORF43 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-EE-A184 TCGA-ER-A195 
       70.16        44.19        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        86.76        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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       21.73        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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
              5.13               0.13 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             70.16             125.65 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
             44.19              16.24 
[1] "5.1 - 70.2 (44.2)"  "0.1 - 125.7 (16.2)"
[1] "hr=" "1.2"
D55V2, survival
                    sevent
clus2                  0   1
  C12ORF43 MUTATED     2   3
  C12ORF43 WILD-TYPE 127 138
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 5                265 
  C12ORF43 MUTATED C12ORF43 WILD-TYPE 
                 3                138 
$`C12ORF43 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-EE-A184 TCGA-ER-A195 
       71.80        62.07        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        86.76        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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  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              51.35 
[1] "35.4 - 71.8 (66.1)" "0.2 - 357.4 (51.4)"
[1] "hr=" "1.2"
D55V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  C12ORF43 MUTATED                    2             0
  C12ORF43 WILD-TYPE                 37             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C12ORF43 MUTATED                                           2
  C12ORF43 WILD-TYPE                                        58
                    vv
clus                 REGIONAL LYMPH NODE
  C12ORF43 MUTATED                     1
  C12ORF43 WILD-TYPE                 170
D55V4, multiclass
                                           clus
vv                                          C12ORF43 MUTATED C12ORF43 WILD-TYPE
  DISTANT METASTASIS                                       2                 37
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                2                 58
  REGIONAL LYMPH NODE                                      1                170
[1] 4 2
[1] 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      24        9       23       16
                    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        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C12ORF43 MUTATED            0          1        0
  C12ORF43 WILD-TYPE         23         45       16
D55V5, multiclass
             clus
vv            C12ORF43 MUTATED C12ORF43 WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    0                 24
  STAGE IA                   1                  9
  STAGE IB                   1                 23
  STAGE II                   0                 16
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  0                  9
  STAGE III                  1                 31
  STAGE IIIA                 0                 13
  STAGE IIIB                 0                 23
  STAGE IIIC                 1                 45
  STAGE IV                   0                 16
[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    51 58 54 56
D55V6, multiclass
       clus
vv      C12ORF43 MUTATED C12ORF43 WILD-TYPE
  T0+T1                1                 51
  T2                   1                 58
  T3                   0                 54
  T4                   1                 56
[1] 4 2
[1] TRUE
[1] "dimension of 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 136  47  33  35
D55V7, multiclass
    clus
vv   C12ORF43 MUTATED C12ORF43 WILD-TYPE
  N0                3                136
  N1                1                 47
  N2                0                 33
  N3                1                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  C12ORF43 MUTATED     5   0   0   0   0
  C12ORF43 WILD-TYPE 239   4   3   2   8
D55V8, multiclass
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  M0                 5                239
  M1                 0                  4
  M1A                0                  3
  M1B                0                  2
  M1C                0                  8
[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 101  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      2    1
  C12ORF43 WILD-TYPE  101   67
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  NO                 2                101
  YES                1                 67
[1] 2 2
[1] FALSE
D55V10, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     0   5
  C12ORF43 WILD-TYPE  36 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    5
  C12ORF43 WILD-TYPE   36  234
     clus
vv    C12ORF43 MUTATED C12ORF43 WILD-TYPE
  NO                 0                 36
  YES                5                234
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     1   4
  C12ORF43 WILD-TYPE 105 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      1    4
  C12ORF43 WILD-TYPE  105  166
        clus
vv       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  FEMALE                1                105
  MALE                  4                166
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C12ORF43 MUTATED       0                         0     5
  C12ORF43 WILD-TYPE     3                         1   267
D55V13, multiclass
                           clus
vv                          C12ORF43 MUTATED C12ORF43 WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                    cls
clus                   0   1
  C12ORF43 MUTATED     0   5
  C12ORF43 WILD-TYPE   3 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF43 MUTATED      0    5
  C12ORF43 WILD-TYPE    3  264
                        clus
vv                       C12ORF43 MUTATED C12ORF43 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                264
[1] 2 2
[1] FALSE

Clustering(56) Variable = XIRP2 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2              0  1
  XIRP2 MUTATED   45 43
  XIRP2 WILD-TYPE 81 97
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             88             178 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             43              97 
$`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        29.23        32.61        25.78        52.01        47.87 
TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
       17.72         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 
       62.79        36.85         1.08        39.62        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        36.30        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        55.69         1.15        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MR 
        8.84        47.51         9.53         2.73        44.25        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J4 
       53.16        52.67        51.62        30.15        15.95        22.92 
TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       21.60         0.95        27.35        31.40        18.61        38.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1Z3 
        3.52        11.90        11.80        12.62        11.74        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 
        7.30         3.39        12.89         8.65         5.23        53.85 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       28.73        10.78         6.41         2.27         0.99         0.13 
TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
        0.16        11.61        10.13        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        86.76        44.19         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        59.57       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        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HW 
       21.44        13.68        23.11        21.93        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-EB-A5UL TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 
       23.15        19.00        13.35        10.55         6.31        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        5.13         4.31        60.23        15.85         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29W 
        9.90        37.97         8.55         9.50         8.09        32.15 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
        8.09        49.22         9.67        36.33        51.12        60.00 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP 
       47.21        19.43        16.01        35.54        28.31         5.42 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH 
       13.02        98.27         2.70         6.18        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       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       26.99        21.60         5.56       124.31       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       13.81        12.72         3.22        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       18.41        21.73        33.60        12.95         5.72        76.41 
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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        6.58        17.72        78.44         1.87         1.51        13.08 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       15.52         7.33        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-A1ZR 
        7.17        30.87        12.92        47.38        52.08         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
       49.15        40.64         8.68        27.39         0.82         7.36 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       14.20         5.98         0.20        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        0.85        44.28        31.33        84.72        16.24        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
           0.13            0.20 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         103.59          125.65 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         14.535          18.410 
[1] "0.1 - 103.6 (14.5)" "0.2 - 125.7 (18.4)"
[1] "hr=" "1"  
D56V2, survival
                 sevent
clus2              0  1
  XIRP2 MUTATED   47 43
  XIRP2 WILD-TYPE 82 98
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             90             180 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             43              98 
$`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        45.30        63.81        26.89       135.75       137.92 
TCGA-D3-A5GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC 
       18.18        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        63.78        64.64         2.60        56.84 
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        36.82 
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       126.81        14.30 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF 
       44.88        94.82        21.67        61.51        47.28       268.73 
TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE 
      103.20       134.40       162.48        71.21        51.62        54.51 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A193 
       23.47       127.20        36.95       201.80        27.35        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A2NC TCGA-ER-A2NG 
       35.44        50.76        12.59        13.02        43.82        31.27 
TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       32.05        20.91        27.72        48.85        23.93       133.55 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.02        77.82        28.73        12.43        49.45        77.88 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       22.92        47.54         0.16        11.74        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        86.76        62.07       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        59.57       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       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 
       22.62       178.32       125.19       151.53         6.41        22.29 
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        68.25        54.02        17.29        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       133.81        91.56 
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       195.02        17.92       102.90        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       161.03       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       158.63       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        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       50.89        37.25         8.88       148.18        79.99        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       20.15        16.37       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59       202.65        28.08         7.79       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-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A5DY 
       27.09        66.67       174.84        26.73         0.20        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       64.44        32.48        39.58         6.67         0.33         0.69 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
           0.16            0.20 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         314.56          357.37 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
          48.13           54.38 
[1] "0.2 - 314.6 (48.1)" "0.2 - 357.4 (54.4)"
[1] "hr=" "1.1"
D56V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  XIRP2 MUTATED                   20             2
  XIRP2 WILD-TYPE                 19             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  XIRP2 MUTATED                                          20                  51
  XIRP2 WILD-TYPE                                        40                 120
D56V4, multiclass
                                           clus
vv                                          XIRP2 MUTATED XIRP2 WILD-TYPE
  DISTANT METASTASIS                                   20              19
  PRIMARY TUMOR                                         2               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            20              40
  REGIONAL LYMPH NODE                                  51             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       7        5        8        9
  XIRP2 WILD-TYPE           7       5      17        5       16        7
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  XIRP2 MUTATED           6         6         2        11          2          7
  XIRP2 WILD-TYPE         4         8         7        21         11         16
                 vv
clus              STAGE IIIC STAGE IV
  XIRP2 MUTATED           15        5
  XIRP2 WILD-TYPE         31       11
D56V5, multiclass
             clus
vv            XIRP2 MUTATED XIRP2 WILD-TYPE
  I OR II NOS             3               7
  STAGE 0                 1               5
  STAGE I                 7              17
  STAGE IA                5               5
  STAGE IB                8              16
  STAGE II                9               7
  STAGE IIA               6               4
  STAGE IIB               6               8
  STAGE IIC               2               7
  STAGE III              11              21
  STAGE IIIA              2              11
  STAGE IIIB              7              16
  STAGE IIIC             15              31
  STAGE IV                5              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
  XIRP2 MUTATED      17 21 22 19
  XIRP2 WILD-TYPE    35 38 32 38
D56V6, multiclass
       clus
vv      XIRP2 MUTATED XIRP2 WILD-TYPE
  T0+T1            17              35
  T2               21              38
  T3               22              32
  T4               19              38
[1] 4 2
[1] TRUE
[1] "dimension of 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   50 17 11  9
  XIRP2 WILD-TYPE 89 31 22 27
D56V7, multiclass
    clus
vv   XIRP2 MUTATED XIRP2 WILD-TYPE
  N0            50              89
  N1            17              31
  N2            11              22
  N3             9              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
  XIRP2 MUTATED    85   1   1   0   3
  XIRP2 WILD-TYPE 159   3   2   2   5
D56V8, multiclass
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  M0             85             159
  M1              1               3
  M1A             1               2
  M1B             0               2
  M1C             3               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"
D56V9, binary
                 cls
clus               0  1
  XIRP2 MUTATED   39 24
  XIRP2 WILD-TYPE 64 44
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     39   24
  XIRP2 WILD-TYPE   64   44
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO             39              64
  YES            24              44
[1] 2 2
[1] FALSE
D56V10, binary
                 cls
clus                0   1
  XIRP2 MUTATED    10  83
  XIRP2 WILD-TYPE  26 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     10   83
  XIRP2 WILD-TYPE   26  156
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO             10              26
  YES            83             156
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, binary
                 cls
clus                0   1
  XIRP2 MUTATED    39  54
  XIRP2 WILD-TYPE  67 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     39   54
  XIRP2 WILD-TYPE   67  116
        clus
vv       XIRP2 MUTATED XIRP2 WILD-TYPE
  FEMALE            39              67
  MALE              54             116
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XIRP2 MUTATED       0                         0    93
  XIRP2 WILD-TYPE     3                         1   179
D56V13, multiclass
                           clus
vv                          XIRP2 MUTATED XIRP2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                93             179
[1] 3 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  91
  XIRP2 WILD-TYPE   2 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      1   91
  XIRP2 WILD-TYPE    2  178
                        clus
vv                       XIRP2 MUTATED XIRP2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            91             178
[1] 2 2
[1] FALSE

Clustering(57) Variable = USH2A MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2              0  1
  USH2A MUTATED   42 45
  USH2A WILD-TYPE 84 95
  USH2A MUTATED USH2A WILD-TYPE 
             87             179 
  USH2A MUTATED USH2A WILD-TYPE 
             45              95 
$`USH2A MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MV 
       11.41        36.16        59.57        46.98       103.59        29.23 
TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       54.31        25.78        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-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C 
       13.35         1.12         1.35         4.31         4.34        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15        62.79         1.08        39.62         9.50        12.03 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GJ 
        9.99         2.43        11.31        49.22        36.33        19.43 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       28.31        55.69         1.15        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       47.51         9.53        14.56        63.42       111.91        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        60.49        53.16       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD 
        3.68        13.81        22.92        21.60        16.14        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E 
       18.41        31.40        38.40         5.72         3.78        11.90 
TCGA-ER-A19F TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z3 
       11.11        36.07        11.80         1.71        85.74        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZW 
        7.30        20.38        12.89        47.38         8.81        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A3OT 
        5.23        53.85         2.27         0.99         0.13         9.90 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-QB-A6FS 
       11.61        10.13         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        86.76        44.19 
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        93.21        54.74        31.30 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       32.28        21.44        32.61        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I1 
       23.11         4.01        21.93         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        23.15        19.00 
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        60.23        15.85         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        36.85         8.09         8.84        32.15 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
        8.09        36.30         9.67        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       60.00        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP 
        2.73        44.25         7.96       125.65        25.08        26.99 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       52.67         5.56        30.15        15.95        12.72         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       21.60        22.22         0.95        21.73        33.60        18.61 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
       12.95        76.41        25.18         3.52       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        6.58        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-A42K 
       12.62        11.74         9.04         6.58        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       18.41        15.72        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       15.52         7.33         3.39         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        7.17        30.87        12.92        52.08         8.65        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       40.64         8.68         0.82         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       10.78         5.98         6.41         0.20         0.16        17.33 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23         0.85        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         0.33         0.69 

  USH2A MUTATED USH2A WILD-TYPE 
           0.13            0.16 
  USH2A MUTATED USH2A WILD-TYPE 
         124.31          125.65 
  USH2A MUTATED USH2A WILD-TYPE 
          14.83           17.56 
[1] "0.1 - 124.3 (14.8)" "0.2 - 125.7 (17.6)"
[1] "hr=" "1"  
D57V2, survival
                 sevent
clus2              0  1
  USH2A MUTATED   42 45
  USH2A WILD-TYPE 87 96
  USH2A MUTATED USH2A WILD-TYPE 
             87             183 
  USH2A MUTATED USH2A WILD-TYPE 
             45              96 
$`USH2A MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MV 
       11.87        42.08        59.57        46.98       103.59        45.30 
TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
      145.12        26.89       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 
       17.29        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        63.78         2.60        56.84        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        86.14        89.33 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       75.48       126.81        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       134.40       162.48       124.31       122.73        51.62 
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 
       51.35        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-GF-A6C9 TCGA-GN-A266 TCGA-QB-A6FS 
       11.74        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        86.76        62.07 
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       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62        63.81       135.75       178.32        18.18 
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 
       22.29         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        68.25        54.02        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       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       91.56       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 
       64.64        37.35        14.47       195.02        17.92        36.82 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        59.28        67.43       314.56       161.03       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-A2MF TCGA-EE-A2MG 
       44.88       129.27        28.83       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
       16.96       158.63        47.54       248.65        71.21        53.26 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       54.51        23.47       138.81       172.18        64.08        53.19 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
      201.80       109.58       148.08        35.44        13.94        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       98.40        12.59       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.05       162.08        50.89         8.88       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-A42K TCGA-FR-A3YN TCGA-FR-A69P 
      247.04        80.32        46.98         6.77        92.98        15.72 
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-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-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        74.73       133.55       148.80        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.09        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
       49.45         0.20         0.16        19.30         7.23         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       39.58         0.33         0.69 

  USH2A MUTATED USH2A WILD-TYPE 
           2.60            0.16 
  USH2A MUTATED USH2A WILD-TYPE 
         357.37          314.56 
  USH2A MUTATED USH2A WILD-TYPE 
          46.82           55.59 
[1] "2.6 - 357.4 (46.8)" "0.2 - 314.6 (55.6)"
[1] "hr=" "1.2"
D57V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  USH2A MUTATED                   14             2
  USH2A WILD-TYPE                 25             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  USH2A MUTATED                                          20                  55
  USH2A WILD-TYPE                                        40                 116
D57V4, multiclass
                                           clus
vv                                          USH2A MUTATED USH2A WILD-TYPE
  DISTANT METASTASIS                                   14              25
  PRIMARY TUMOR                                         2               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            20              40
  REGIONAL LYMPH NODE                                  55             116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              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      19        7       18        5
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  USH2A MUTATED           2         4         2        14          3         10
  USH2A WILD-TYPE         8        10         7        18         10         13
                 vv
clus              STAGE IIIC STAGE IV
  USH2A MUTATED           16        4
  USH2A WILD-TYPE         30       12
D57V5, multiclass
             clus
vv            USH2A MUTATED USH2A WILD-TYPE
  I OR II NOS             4               6
  STAGE 0                 2               4
  STAGE I                 5              19
  STAGE IA                3               7
  STAGE IB                6              18
  STAGE II               11               5
  STAGE IIA               2               8
  STAGE IIB               4              10
  STAGE IIC               2               7
  STAGE III              14              18
  STAGE IIIA              3              10
  STAGE IIIB             10              13
  STAGE IIIC             16              30
  STAGE IV                4              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
  USH2A MUTATED      16 19 21 19
  USH2A WILD-TYPE    36 40 33 38
D57V6, multiclass
       clus
vv      USH2A MUTATED USH2A WILD-TYPE
  T0+T1            16              36
  T2               19              40
  T3               21              33
  T4               19              38
[1] 4 2
[1] TRUE
[1] "dimension of 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 17 14 11
  USH2A WILD-TYPE 97 31 19 25
D57V7, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  N0            42              97
  N1            17              31
  N2            14              19
  N3            11              25
[1] 4 2
[1] 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   1
  USH2A WILD-TYPE 161   3   1   2   7
D57V8, multiclass
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  M0             83             161
  M1              1               3
  M1A             2               1
  M1B             0               2
  M1C             1               7
[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 72 46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     31   22
  USH2A WILD-TYPE   72   46
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             31              72
  YES            22              46
[1] 2 2
[1] FALSE
D57V10, binary
                 cls
clus                0   1
  USH2A MUTATED    17  74
  USH2A WILD-TYPE  19 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     17   74
  USH2A WILD-TYPE   19  165
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             17              19
  YES            74             165
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, binary
                 cls
clus                0   1
  USH2A MUTATED    30  61
  USH2A WILD-TYPE  76 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     30   61
  USH2A WILD-TYPE   76  109
        clus
vv       USH2A MUTATED USH2A WILD-TYPE
  FEMALE            30              76
  MALE              61             109
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USH2A MUTATED       0                         0    91
  USH2A WILD-TYPE     3                         1   181
D57V13, multiclass
                           clus
vv                          USH2A MUTATED USH2A WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                91             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"
D57V14, binary
                 cls
clus                0   1
  USH2A MUTATED     1  90
  USH2A WILD-TYPE   2 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED      1   90
  USH2A WILD-TYPE    2  179
                        clus
vv                       USH2A MUTATED USH2A WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            90             179
[1] 2 2
[1] FALSE

Clustering(58) Variable = DDX3X MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  DDX3X MUTATED     9   9
  DDX3X WILD-TYPE 117 131
  DDX3X MUTATED DDX3X WILD-TYPE 
             18             248 
  DDX3X MUTATED DDX3X WILD-TYPE 
              9             131 
$`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        60.23        62.79 
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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31         4.34        15.85         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        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43        32.15         8.09        11.31        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        17.98        60.00        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR 
       19.43        16.01        35.54        28.31        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
       26.99        21.60        60.49        53.16        52.67       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        30.15        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  DDX3X MUTATED DDX3X WILD-TYPE 
           5.42            0.13 
  DDX3X MUTATED DDX3X WILD-TYPE 
         124.31          125.65 
  DDX3X MUTATED DDX3X WILD-TYPE 
         18.215          16.900 
[1] "5.4 - 124.3 (18.2)" "0.1 - 125.7 (16.9)"
[1] "hr=" "1.3"
D58V2, survival
                 sevent
clus2               0   1
  DDX3X MUTATED    10   9
  DDX3X WILD-TYPE 119 132
  DDX3X MUTATED DDX3X WILD-TYPE 
             19             251 
  DDX3X MUTATED DDX3X WILD-TYPE 
              9             132 
$`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       133.81 
TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2ML 
       63.78       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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29 
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        91.56 
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        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       46.82        36.82        39.29        86.14        59.28       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      158.63       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        71.21       122.73        51.62         3.68        54.51 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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-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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  DDX3X MUTATED DDX3X WILD-TYPE 
          13.81            0.16 
  DDX3X MUTATED DDX3X WILD-TYPE 
         203.05          357.37 
  DDX3X MUTATED DDX3X WILD-TYPE 
          63.78           51.35 
[1] "13.8 - 203.1 (63.8)" "0.2 - 357.4 (51.4)" 
[1] "hr=" "1"  
D58V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DDX3X MUTATED                    2             1
  DDX3X WILD-TYPE                 37             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DDX3X MUTATED                                           6                  10
  DDX3X WILD-TYPE                                        54                 161
D58V4, multiclass
                                           clus
vv                                          DDX3X MUTATED DDX3X WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             6              54
  REGIONAL LYMPH NODE                                  10             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
  DDX3X MUTATED             0       0       1        1        2        3
  DDX3X WILD-TYPE          10       6      23        9       22       13
                 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        31         13         20
                 vv
clus              STAGE IIIC STAGE IV
  DDX3X MUTATED            2        2
  DDX3X WILD-TYPE         44       14
D58V5, multiclass
             clus
vv            DDX3X MUTATED DDX3X WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                1               9
  STAGE IB                2              22
  STAGE II                3              13
  STAGE IIA               1               9
  STAGE IIB               2              12
  STAGE IIC               0               9
  STAGE III               1              31
  STAGE IIIA              0              13
  STAGE IIIB              3              20
  STAGE IIIC              2              44
  STAGE IV                2              14
[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    49 54 49 53
D58V6, multiclass
       clus
vv      DDX3X MUTATED DDX3X WILD-TYPE
  T0+T1             3              49
  T2                5              54
  T3                5              49
  T4                4              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
  DDX3X MUTATED    11   2   2   4
  DDX3X WILD-TYPE 128  46  31  32
D58V7, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  N0            11             128
  N1             2              46
  N2             2              31
  N3             4              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
  DDX3X MUTATED    16   1   1   1   0
  DDX3X WILD-TYPE 228   3   2   1   8
D58V8, multiclass
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  M0             16             228
  M1              1               3
  M1A             1               2
  M1B             1               1
  M1C             0               8
[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 94 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      9    5
  DDX3X WILD-TYPE   94   63
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              9              94
  YES             5              63
[1] 2 2
[1] FALSE
D58V10, binary
                 cls
clus                0   1
  DDX3X MUTATED     3  16
  DDX3X WILD-TYPE  33 223
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      3   16
  DDX3X WILD-TYPE   33  223
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              3              33
  YES            16             223
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, binary
                 cls
clus                0   1
  DDX3X MUTATED     3  16
  DDX3X WILD-TYPE 103 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      3   16
  DDX3X WILD-TYPE  103  154
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  FEMALE             3             103
  MALE              16             154
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX3X MUTATED       0                         0    19
  DDX3X WILD-TYPE     3                         1   253
D58V13, multiclass
                           clus
vv                          DDX3X MUTATED DDX3X WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                19             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"
D58V14, binary
                 cls
clus                0   1
  DDX3X MUTATED     0  19
  DDX3X WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      0   19
  DDX3X WILD-TYPE    3  250
                        clus
vv                       DDX3X MUTATED DDX3X WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            19             250
[1] 2 2
[1] FALSE

Clustering(59) Variable = PTPN22 MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2                0   1
  PTPN22 MUTATED    17   7
  PTPN22 WILD-TYPE 109 133
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              24              242 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
               7              133 
$`PTPN22 MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GO 
       22.55        86.76        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        19.00        12.20        62.79        56.02        60.49 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19N 
      124.31        13.81        15.95        22.22         0.95        42.84 
TCGA-FS-A1ZW TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 TCGA-RP-A693 TCGA-RP-A694 
       27.39         6.41         0.99        10.13         0.33         0.69 

$`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        44.19         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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN 
       14.83        13.15         0.20        23.15        13.35        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        60.23         4.34        15.85         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 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
        7.96        14.56        63.42       125.65       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       26.99        21.60        53.16        52.67         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         3.68        30.15        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        21.60        16.14        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-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-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  PTPN22 MUTATED PTPN22 WILD-TYPE 
            0.33             0.13 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
          124.31           125.65 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
          22.385           16.190 
[1] "0.3 - 124.3 (22.4)" "0.1 - 125.7 (16.2)"
[1] "hr=" "2.1"
D59V2, survival
                  sevent
clus2                0   1
  PTPN22 MUTATED    17   7
  PTPN22 WILD-TYPE 112 134
  PTPN22 MUTATED PTPN22 WILD-TYPE 
              24              246 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
               7              134 
$`PTPN22 MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A5GO 
       31.59        86.76        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        54.02        26.89        63.78       167.90       134.40 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19N 
      124.31        13.81        23.47        53.19       201.80        44.05 
TCGA-FS-A1ZW TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A266 TCGA-RP-A693 TCGA-RP-A694 
       49.48        49.45        22.92        10.13         0.33         0.69 

$`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        62.07       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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      135.75       178.32        18.18       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        22.29         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        68.25        17.29        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 
      133.81       151.27        91.56       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        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       203.05        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21        53.26       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       54.51       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        51.35       109.58       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-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        77.88         0.20        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 

  PTPN22 MUTATED PTPN22 WILD-TYPE 
            0.33             0.16 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
          201.80           357.37 
  PTPN22 MUTATED PTPN22 WILD-TYPE 
          49.465           52.585 
[1] "0.3 - 201.8 (49.5)" "0.2 - 357.4 (52.6)"
[1] "hr=" "1.6"
D59V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PTPN22 MUTATED                    3             1
  PTPN22 WILD-TYPE                 36             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PTPN22 MUTATED                                           6
  PTPN22 WILD-TYPE                                        54
                  vv
clus               REGIONAL LYMPH NODE
  PTPN22 MUTATED                    14
  PTPN22 WILD-TYPE                 157
D59V4, multiclass
                                           clus
vv                                          PTPN22 MUTATED PTPN22 WILD-TYPE
  DISTANT METASTASIS                                     3               36
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              6               54
  REGIONAL LYMPH NODE                                   14              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
  PTPN22 MUTATED             0       1       2        0        2        1
  PTPN22 WILD-TYPE          10       5      22       10       22       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PTPN22 MUTATED           1         0         0         7          2
  PTPN22 WILD-TYPE         9        14         9        25         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PTPN22 MUTATED            3          1        2
  PTPN22 WILD-TYPE         20         45       14
D59V5, multiclass
             clus
vv            PTPN22 MUTATED PTPN22 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  2               22
  STAGE IA                 0               10
  STAGE IB                 2               22
  STAGE II                 1               15
  STAGE IIA                1                9
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                7               25
  STAGE IIIA               2               11
  STAGE IIIB               3               20
  STAGE IIIC               1               45
  STAGE IV                 2               14
[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  5  3
  PTPN22 WILD-TYPE    46 55 49 54
D59V6, multiclass
       clus
vv      PTPN22 MUTATED PTPN22 WILD-TYPE
  T0+T1              6               46
  T2                 4               55
  T3                 5               49
  T4                 3               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
  PTPN22 MUTATED     8   5   6   1
  PTPN22 WILD-TYPE 131  43  27  35
D59V7, multiclass
    clus
vv   PTPN22 MUTATED PTPN22 WILD-TYPE
  N0              8              131
  N1              5               43
  N2              6               27
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  PTPN22 MUTATED    20   0   0   0   2
  PTPN22 WILD-TYPE 224   4   3   2   6
D59V8, multiclass
     clus
vv    PTPN22 MUTATED PTPN22 WILD-TYPE
  M0              20              224
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              2                6
[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 96 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      7    3
  PTPN22 WILD-TYPE   96   65
     clus
vv    PTPN22 MUTATED PTPN22 WILD-TYPE
  NO               7               96
  YES              3               65
[1] 2 2
[1] FALSE
D59V10, binary
                  cls
clus                 0   1
  PTPN22 MUTATED     9  15
  PTPN22 WILD-TYPE  27 224
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      9   15
  PTPN22 WILD-TYPE   27  224
     clus
vv    PTPN22 MUTATED PTPN22 WILD-TYPE
  NO               9               27
  YES             15              224
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, binary
                  cls
clus                 0   1
  PTPN22 MUTATED     7  17
  PTPN22 WILD-TYPE  99 153
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      7   17
  PTPN22 WILD-TYPE   99  153
        clus
vv       PTPN22 MUTATED PTPN22 WILD-TYPE
  FEMALE              7               99
  MALE               17              153
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN22 MUTATED       0                         0    24
  PTPN22 WILD-TYPE     3                         1   248
D59V13, multiclass
                           clus
vv                          PTPN22 MUTATED PTPN22 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 24              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"
D59V14, binary
                  cls
clus                 0   1
  PTPN22 MUTATED     0  24
  PTPN22 WILD-TYPE   3 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN22 MUTATED      0   24
  PTPN22 WILD-TYPE    3  245
                        clus
vv                       PTPN22 MUTATED PTPN22 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             24              245
[1] 2 2
[1] FALSE

Clustering(60) Variable = C3ORF71 MUTATION ANALYSIS
D60V1, survival
                   sevent
clus2                 0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 125 137
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               262 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                3               137 
$`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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       30.08        19.43        16.01        28.31        33.83        55.69 
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-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       98.27         2.70         6.18         9.53        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
            11.80              0.13 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
            47.51            125.65 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
           33.980            16.355 
[1] "11.8 - 47.5 (34.0)" "0.1 - 125.7 (16.4)"
[1] "hr=" "1.1"
D60V2, survival
                   sevent
clus2                 0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 128 138
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               266 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                3               138 
$`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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  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            51.485 
[1] "43.8 - 112.6 (70.6)" "0.2 - 357.4 (51.5)" 
[1] "hr=" "1.4"
D60V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  C3ORF71 MUTATED                    1             0
  C3ORF71 WILD-TYPE                 38             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C3ORF71 MUTATED                                           0
  C3ORF71 WILD-TYPE                                        60
                   vv
clus                REGIONAL LYMPH NODE
  C3ORF71 MUTATED                     3
  C3ORF71 WILD-TYPE                 168
D60V4, multiclass
                                           clus
vv                                          C3ORF71 MUTATED C3ORF71 WILD-TYPE
  DISTANT METASTASIS                                      1                38
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               0                60
  REGIONAL LYMPH NODE                                     3               168
[1] 4 2
[1] 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      23       10       23       16
                   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        32         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C3ORF71 MUTATED            0          0        0
  C3ORF71 WILD-TYPE         23         46       16
D60V5, multiclass
             clus
vv            C3ORF71 MUTATED C3ORF71 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   1                23
  STAGE IA                  0                10
  STAGE IB                  1                23
  STAGE II                  0                16
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 0                32
  STAGE IIIA                0                13
  STAGE IIIB                0                23
  STAGE IIIC                0                46
  STAGE IV                  0                16
[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    52 57 53 57
D60V6, multiclass
       clus
vv      C3ORF71 MUTATED C3ORF71 WILD-TYPE
  T0+T1               0                52
  T2                  2                57
  T3                  1                53
  T4                  0                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C3ORF71 MUTATED     4   0   0   0
  C3ORF71 WILD-TYPE 135  48  33  36
D60V7, multiclass
    clus
vv   C3ORF71 MUTATED C3ORF71 WILD-TYPE
  N0               4               135
  N1               0                48
  N2               0                33
  N3               0                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                 M0  M1 M1A M1B M1C
  C3ORF71 MUTATED     4   0   0   0   0
  C3ORF71 WILD-TYPE 240   4   3   2   8
D60V8, multiclass
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  M0                4               240
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 100  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      3    0
  C3ORF71 WILD-TYPE  100   68
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  NO                3               100
  YES               0                68
[1] 2 2
[1] FALSE
D60V10, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     0   4
  C3ORF71 WILD-TYPE  36 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      0    4
  C3ORF71 WILD-TYPE   36  235
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  NO                0                36
  YES               4               235
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 105 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      1    3
  C3ORF71 WILD-TYPE  105  167
        clus
vv       C3ORF71 MUTATED C3ORF71 WILD-TYPE
  FEMALE               1               105
  MALE                 3               167
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3ORF71 MUTATED       0                         0     4
  C3ORF71 WILD-TYPE     3                         1   268
D60V13, multiclass
                           clus
vv                          C3ORF71 MUTATED C3ORF71 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4               268
[1] 3 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   3 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      0    4
  C3ORF71 WILD-TYPE    3  265
                        clus
vv                       C3ORF71 MUTATED C3ORF71 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               265
[1] 2 2
[1] FALSE

Clustering(61) Variable = CEACAM6 MUTATION ANALYSIS
D61V1, survival
                   sevent
clus2                 0   1
  CEACAM6 MUTATED     4  11
  CEACAM6 WILD-TYPE 122 129
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               251 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               11               129 
$`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        53.16        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87        13.68        17.72        23.11        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       13.22        11.57        10.55         6.31         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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55        36.85        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        47.21        30.08        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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 
       60.49        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        21.60        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
        5.72        25.18         3.78         3.52        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
        9.57        36.07         6.58        17.72        78.44         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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82         5.23         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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
             1.08              0.13 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
            76.41            125.65 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
            12.72             17.56 
[1] "1.1 - 76.4 (12.7)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.5"
D61V2, survival
                   sevent
clus2                 0   1
  CEACAM6 MUTATED     4  11
  CEACAM6 WILD-TYPE 125 130
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               15               255 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
               11               130 
$`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       162.48       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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       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       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
             2.60              0.16 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
           162.48            357.37 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
            67.43             51.62 
[1] "2.6 - 162.5 (67.4)" "0.2 - 357.4 (51.6)"
[1] "hr=" "1.7"
D61V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  CEACAM6 MUTATED                    2             0
  CEACAM6 WILD-TYPE                 37             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CEACAM6 MUTATED                                           4
  CEACAM6 WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  CEACAM6 MUTATED                     9
  CEACAM6 WILD-TYPE                 162
D61V4, multiclass
                                           clus
vv                                          CEACAM6 MUTATED CEACAM6 WILD-TYPE
  DISTANT METASTASIS                                      2                37
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                56
  REGIONAL LYMPH NODE                                     9               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
  CEACAM6 MUTATED             0       0       0        1        2        3
  CEACAM6 WILD-TYPE          10       6      24        9       22       13
                   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        30         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  CEACAM6 MUTATED            0          2        1
  CEACAM6 WILD-TYPE         23         44       15
D61V5, multiclass
             clus
vv            CEACAM6 MUTATED CEACAM6 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   0                24
  STAGE IA                  1                 9
  STAGE IB                  2                22
  STAGE II                  3                13
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 0                 9
  STAGE III                 2                30
  STAGE IIIA                1                12
  STAGE IIIB                0                23
  STAGE IIIC                2                44
  STAGE IV                  1                15
[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    51 56 50 52
D61V6, multiclass
       clus
vv      CEACAM6 MUTATED CEACAM6 WILD-TYPE
  T0+T1               1                51
  T2                  3                56
  T3                  4                50
  T4                  5                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
  CEACAM6 MUTATED    11   1   0   2
  CEACAM6 WILD-TYPE 128  47  33  34
D61V7, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  N0              11               128
  N1               1                47
  N2               0                33
  N3               2                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  CEACAM6 MUTATED    13   1   0   0   0
  CEACAM6 WILD-TYPE 231   3   3   2   8
D61V8, multiclass
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  M0               13               231
  M1                1                 3
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 94 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      9    2
  CEACAM6 WILD-TYPE   94   66
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  NO                9                94
  YES               2                66
[1] 2 2
[1] FALSE
D61V10, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     2  13
  CEACAM6 WILD-TYPE  34 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      2   13
  CEACAM6 WILD-TYPE   34  226
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  NO                2                34
  YES              13               226
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     3  12
  CEACAM6 WILD-TYPE 103 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      3   12
  CEACAM6 WILD-TYPE  103  158
        clus
vv       CEACAM6 MUTATED CEACAM6 WILD-TYPE
  FEMALE               3               103
  MALE                12               158
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEACAM6 MUTATED       0                         0    15
  CEACAM6 WILD-TYPE     3                         1   257
D61V13, multiclass
                           clus
vv                          CEACAM6 MUTATED CEACAM6 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  15               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"
D61V14, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     0  15
  CEACAM6 WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      0   15
  CEACAM6 WILD-TYPE    3  254
                        clus
vv                       CEACAM6 MUTATED CEACAM6 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               254
[1] 2 2
[1] FALSE

Clustering(62) Variable = MUC7 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  MUC7 MUTATED    10   7
  MUC7 WILD-TYPE 116 133
  MUC7 MUTATED MUC7 WILD-TYPE 
            17            249 
  MUC7 MUTATED MUC7 WILD-TYPE 
             7            133 
$`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 
       62.79        34.29        19.43        55.69        60.49        53.16 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-FS-A1ZK TCGA-FS-A4FC TCGA-GF-A6C9 
       21.60        21.60        12.89         6.41        11.61 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23        15.85         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        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        17.98        60.00        47.21        30.08 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       111.91        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        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       12.72         3.22        22.92        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         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 
       17.33         9.90         7.23         0.85        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  MUC7 MUTATED MUC7 WILD-TYPE 
          1.12           0.13 
  MUC7 MUTATED MUC7 WILD-TYPE 
         62.79         125.65 
  MUC7 MUTATED MUC7 WILD-TYPE 
         19.43          16.47 
[1] "1.1 - 62.8 (19.4)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.3"
D62V2, survival
                sevent
clus2              0   1
  MUC7 MUTATED    10   7
  MUC7 WILD-TYPE 119 134
  MUC7 MUTATED MUC7 WILD-TYPE 
            17            253 
  MUC7 MUTATED MUC7 WILD-TYPE 
             7            134 
$`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 
       63.78        67.43        89.33       126.81       134.40       162.48 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-FS-A1ZK TCGA-FS-A4FC TCGA-GF-A6C9 
       36.95        64.08        23.93        49.45        11.74 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23        71.21        53.26       124.31       122.73        51.62 
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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-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-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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         2.04       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  MUC7 MUTATED MUC7 WILD-TYPE 
         11.74           0.16 
  MUC7 MUTATED MUC7 WILD-TYPE 
        162.48         357.37 
  MUC7 MUTATED MUC7 WILD-TYPE 
         66.25          50.89 
[1] "11.7 - 162.5 (66.2)" "0.2 - 357.4 (50.9)" 
[1] "hr=" "1.4"
D62V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MUC7 MUTATED                    4             1
  MUC7 WILD-TYPE                 35             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MUC7 MUTATED                                           5                   7
  MUC7 WILD-TYPE                                        55                 164
D62V4, multiclass
                                           clus
vv                                          MUC7 MUTATED MUC7 WILD-TYPE
  DISTANT METASTASIS                                   4             35
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            5             55
  REGIONAL LYMPH NODE                                  7            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
  MUC7 MUTATED             0       1       2        1        0        5
  MUC7 WILD-TYPE          10       5      22        9       24       11
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MUC7 MUTATED           1         1         0         1          1          3
  MUC7 WILD-TYPE         9        13         9        31         12         20
                vv
clus             STAGE IIIC STAGE IV
  MUC7 MUTATED            1        0
  MUC7 WILD-TYPE         45       16
D62V5, multiclass
             clus
vv            MUC7 MUTATED MUC7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                2             22
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               5             11
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              1             31
  STAGE IIIA             1             12
  STAGE IIIB             3             20
  STAGE IIIC             1             45
  STAGE IV               0             16
[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    51 57 45 54
D62V6, multiclass
       clus
vv      MUC7 MUTATED MUC7 WILD-TYPE
  T0+T1            1             51
  T2               2             57
  T3               9             45
  T4               3             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
  MUC7 MUTATED    11   4   1   0
  MUC7 WILD-TYPE 128  44  32  36
D62V7, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  N0           11            128
  N1            4             44
  N2            1             32
  N3            0             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              M0  M1 M1A M1B M1C
  MUC7 MUTATED    16   0   0   0   0
  MUC7 WILD-TYPE 228   4   3   2   8
D62V8, multiclass
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  M0            16            228
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 94 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      9    3
  MUC7 WILD-TYPE   94   65
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO             9             94
  YES            3             65
[1] 2 2
[1] FALSE
D62V10, binary
                cls
clus               0   1
  MUC7 MUTATED     1  16
  MUC7 WILD-TYPE  35 223
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      1   16
  MUC7 WILD-TYPE   35  223
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO             1             35
  YES           16            223
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, binary
                cls
clus               0   1
  MUC7 MUTATED     4  13
  MUC7 WILD-TYPE 102 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      4   13
  MUC7 WILD-TYPE  102  157
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  FEMALE            4            102
  MALE             13            157
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC7 MUTATED       0                         0    17
  MUC7 WILD-TYPE     3                         1   255
D62V13, multiclass
                           clus
vv                          MUC7 MUTATED MUC7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               17            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"
D62V14, binary
                cls
clus               0   1
  MUC7 MUTATED     0  17
  MUC7 WILD-TYPE   3 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      0   17
  MUC7 WILD-TYPE    3  252
                        clus
vv                       MUC7 MUTATED MUC7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           17            252
[1] 2 2
[1] FALSE

Clustering(63) Variable = SELP MUTATION ANALYSIS
D63V1, survival
                sevent
clus2              0   1
  SELP MUTATED    18  14
  SELP WILD-TYPE 108 126
  SELP MUTATED SELP WILD-TYPE 
            32            234 
  SELP MUTATED SELP WILD-TYPE 
            14            126 
$`SELP MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MU TCGA-D3-A5GU 
       28.08        44.19        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        62.79 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2MD 
       39.62         8.84         9.99        51.12        55.69         9.53 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A2NG TCGA-FR-A69P 
       51.62        13.81        31.40        11.90        12.62        15.72 
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 
       17.33        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        86.76        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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87        13.68        17.72         4.01        21.93 
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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       13.22        11.57         6.31         8.12         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        60.23        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        7.99         9.90        37.97         8.55        36.85         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        9.50        12.03         8.09         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       11.31        49.22        36.30         9.67        36.33        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73         3.68        30.15        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       78.44        11.80         1.87         1.51        13.08        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       85.74        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-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.39         0.82         7.36        14.20        10.78         5.98 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.13         0.16         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.85        11.61        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  SELP MUTATED SELP WILD-TYPE 
          0.99           0.13 
  SELP MUTATED SELP WILD-TYPE 
         64.44         125.65 
  SELP MUTATED SELP WILD-TYPE 
        16.525         17.015 
[1] "1.0 - 64.4 (16.5)"  "0.1 - 125.7 (17.0)"
[1] "hr=" "1.2"
D63V2, survival
                sevent
clus2              0   1
  SELP MUTATED    18  14
  SELP WILD-TYPE 111 127
  SELP MUTATED SELP WILD-TYPE 
            32            238 
  SELP MUTATED SELP WILD-TYPE 
            14            127 
$`SELP MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3MU TCGA-D3-A5GU 
       28.08        62.07        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        63.78 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2MD 
       56.84        14.47        55.92        59.28       126.81        47.28 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A2NG TCGA-FR-A69P 
       51.62        13.81        31.40        13.02        31.27        15.72 
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 
       19.30        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        86.76        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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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 
      133.81        91.56       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        64.64         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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        67.43       314.56       161.03 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      162.48        71.21        53.26       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58       148.08        35.44        13.94        50.76         9.17 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        16.37        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       46.98        33.21         6.77        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-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-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-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       47.54         0.16         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  SELP MUTATED SELP WILD-TYPE 
         10.13           0.16 
  SELP MUTATED SELP WILD-TYPE 
        151.27         357.37 
  SELP MUTATED SELP WILD-TYPE 
         36.74          53.97 
[1] "10.1 - 151.3 (36.7)" "0.2 - 357.4 (54.0)" 
[1] "hr=" "1.3"
D63V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  SELP MUTATED                    6             0
  SELP WILD-TYPE                 33             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SELP MUTATED                                           7                  21
  SELP WILD-TYPE                                        53                 150
D63V4, multiclass
                                           clus
vv                                          SELP MUTATED SELP WILD-TYPE
  DISTANT METASTASIS                                   6             33
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            7             53
  REGIONAL LYMPH NODE                                 21            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
  SELP MUTATED             1       1       0        1        4        3
  SELP WILD-TYPE           9       5      24        9       20       13
                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        28         12         18
                vv
clus             STAGE IIIC STAGE IV
  SELP MUTATED            6        2
  SELP WILD-TYPE         40       14
D63V5, multiclass
             clus
vv            SELP MUTATED SELP WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                0             24
  STAGE IA               1              9
  STAGE IB               4             20
  STAGE II               3             13
  STAGE IIA              2              8
  STAGE IIB              3             11
  STAGE IIC              0              9
  STAGE III              4             28
  STAGE IIIA             1             12
  STAGE IIIB             5             18
  STAGE IIIC             6             40
  STAGE IV               2             14
[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    45 54 40 55
D63V6, multiclass
       clus
vv      SELP MUTATED SELP WILD-TYPE
  T0+T1            7             45
  T2               5             54
  T3              14             40
  T4               2             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
  SELP MUTATED    15   7   5   5
  SELP WILD-TYPE 124  41  28  31
D63V7, multiclass
    clus
vv   SELP MUTATED SELP WILD-TYPE
  N0           15            124
  N1            7             41
  N2            5             28
  N3            5             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
  SELP MUTATED    29   0   0   1   1
  SELP WILD-TYPE 215   4   3   1   7
D63V8, multiclass
     clus
vv    SELP MUTATED SELP WILD-TYPE
  M0            29            215
  M1             0              4
  M1A            0              3
  M1B            1              1
  M1C            1              7
[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 91 59
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     12    9
  SELP WILD-TYPE   91   59
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO            12             91
  YES            9             59
[1] 2 2
[1] FALSE
D63V10, binary
                cls
clus               0   1
  SELP MUTATED     7  27
  SELP WILD-TYPE  29 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      7   27
  SELP WILD-TYPE   29  212
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO             7             29
  YES           27            212
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, binary
                cls
clus               0   1
  SELP MUTATED    18  16
  SELP WILD-TYPE  88 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     18   16
  SELP WILD-TYPE   88  154
        clus
vv       SELP MUTATED SELP WILD-TYPE
  FEMALE           18             88
  MALE             16            154
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SELP MUTATED       1                         0    33
  SELP WILD-TYPE     2                         1   239
D63V13, multiclass
                           clus
vv                          SELP MUTATED SELP WILD-TYPE
  ASIAN                                1              2
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               33            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"
D63V14, binary
                cls
clus               0   1
  SELP MUTATED     1  32
  SELP WILD-TYPE   2 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      1   32
  SELP WILD-TYPE    2  237
                        clus
vv                       SELP MUTATED SELP WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           32            237
[1] 2 2
[1] FALSE

Clustering(64) Variable = LIPH MUTATION ANALYSIS
D64V1, survival
                sevent
clus2              0   1
  LIPH MUTATED     9   6
  LIPH WILD-TYPE 117 134
  LIPH MUTATED LIPH WILD-TYPE 
            15            251 
  LIPH MUTATED LIPH WILD-TYPE 
             6            134 
$`LIPH MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A5GO TCGA-D9-A6EC TCGA-EE-A181 
       86.76        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 
       62.79         1.08         9.99         5.42        47.51        52.67 
TCGA-EE-A3JB TCGA-FW-A3R5 TCGA-RP-A694 
        0.95         0.99         0.69 

$`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        44.19 
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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.61        25.78        52.01        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01        21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15         8.55        36.85        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18         9.53        29.46         2.73        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       125.65       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        60.49        53.16         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       15.42        12.16        14.70         5.79         0.33 

  LIPH MUTATED LIPH WILD-TYPE 
          0.69           0.13 
  LIPH MUTATED LIPH WILD-TYPE 
         86.76         125.65 
  LIPH MUTATED LIPH WILD-TYPE 
          9.99          17.56 
[1] "0.7 - 86.8 (10.0)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.1"
D64V2, survival
                sevent
clus2              0   1
  LIPH MUTATED     9   6
  LIPH WILD-TYPE 120 135
  LIPH MUTATED LIPH WILD-TYPE 
            15            255 
  LIPH MUTATED LIPH WILD-TYPE 
             6            135 
$`LIPH MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A5GO TCGA-D9-A6EC TCGA-EE-A181 
       86.76        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 
       63.78         2.60        55.92        13.91        61.51        71.21 
TCGA-EE-A3JB TCGA-FW-A3R5 TCGA-RP-A694 
      201.80        22.92         0.69 

$`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        62.07 
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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81        26.89       135.75       178.32        18.18       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        22.29 
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        68.25        54.02        17.29 
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       133.81       151.27        91.56 
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        64.64        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        53.26       124.31       122.73        51.62 
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 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 
       39.58         6.67         0.33 

  LIPH MUTATED LIPH WILD-TYPE 
          0.69           0.16 
  LIPH MUTATED LIPH WILD-TYPE 
        201.80         357.37 
  LIPH MUTATED LIPH WILD-TYPE 
         61.51          51.35 
[1] "0.7 - 201.8 (61.5)" "0.2 - 357.4 (51.4)"
[1] "hr=" "1.1"
D64V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  LIPH MUTATED                    2             1
  LIPH WILD-TYPE                 37             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  LIPH MUTATED                                           3                   9
  LIPH WILD-TYPE                                        57                 162
D64V4, multiclass
                                           clus
vv                                          LIPH MUTATED LIPH WILD-TYPE
  DISTANT METASTASIS                                   2             37
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             57
  REGIONAL LYMPH NODE                                  9            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
  LIPH MUTATED             0       0       1        0        1        2
  LIPH WILD-TYPE          10       6      23       10       23       14
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LIPH MUTATED           1         0         0         3          2          2
  LIPH WILD-TYPE         9        14         9        29         11         21
                vv
clus             STAGE IIIC STAGE IV
  LIPH MUTATED            2        1
  LIPH WILD-TYPE         44       15
D64V5, multiclass
             clus
vv            LIPH MUTATED LIPH WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                1             23
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               2             14
  STAGE IIA              1              9
  STAGE IIB              0             14
  STAGE IIC              0              9
  STAGE III              3             29
  STAGE IIIA             2             11
  STAGE IIIB             2             21
  STAGE IIIC             2             44
  STAGE IV               1             15
[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  6  3
  LIPH WILD-TYPE    51 57 48 54
D64V6, multiclass
       clus
vv      LIPH MUTATED LIPH WILD-TYPE
  T0+T1            1             51
  T2               2             57
  T3               6             48
  T4               3             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
  LIPH MUTATED     5   4   3   2
  LIPH WILD-TYPE 134  44  30  34
D64V7, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  N0            5            134
  N1            4             44
  N2            3             30
  N3            2             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  LIPH MUTATED    14   0   0   0   1
  LIPH WILD-TYPE 230   4   3   2   7
D64V8, multiclass
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  M0            14            230
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            1              7
[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 97 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      6    3
  LIPH WILD-TYPE   97   65
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO             6             97
  YES            3             65
[1] 2 2
[1] FALSE
D64V10, binary
                cls
clus               0   1
  LIPH MUTATED     2  13
  LIPH WILD-TYPE  34 226
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      2   13
  LIPH WILD-TYPE   34  226
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO             2             34
  YES           13            226
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, binary
                cls
clus               0   1
  LIPH MUTATED     5  10
  LIPH WILD-TYPE 101 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      5   10
  LIPH WILD-TYPE  101  160
        clus
vv       LIPH MUTATED LIPH WILD-TYPE
  FEMALE            5            101
  MALE             10            160
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LIPH MUTATED       0                         0    15
  LIPH WILD-TYPE     3                         1   257
D64V13, multiclass
                           clus
vv                          LIPH MUTATED LIPH WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               15            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"
D64V14, binary
                cls
clus               0   1
  LIPH MUTATED     0  15
  LIPH WILD-TYPE   3 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      0   15
  LIPH WILD-TYPE    3  254
                        clus
vv                       LIPH MUTATED LIPH WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           15            254
[1] 2 2
[1] FALSE

Clustering(65) Variable = MMP1 MUTATION ANALYSIS
D65V1, survival
                sevent
clus2              0   1
  MMP1 MUTATED     6   8
  MMP1 WILD-TYPE 120 132
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            252 
  MMP1 MUTATED MMP1 WILD-TYPE 
             8            132 
$`MMP1 MUTATED`
TCGA-D3-A51F TCGA-D9-A6EC TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       54.74        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 
       55.69         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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        13.22 
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-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31        60.23        15.85         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        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       60.49        53.16        52.67       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  MMP1 MUTATED MMP1 WILD-TYPE 
          0.99           0.13 
  MMP1 MUTATED MMP1 WILD-TYPE 
         55.69         125.65 
  MMP1 MUTATED MMP1 WILD-TYPE 
         12.97          17.64 
[1] "1.0 - 55.7 (13.0)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.2"
D65V2, survival
                sevent
clus2              0   1
  MMP1 MUTATED     6   8
  MMP1 WILD-TYPE 123 133
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            256 
  MMP1 MUTATED MMP1 WILD-TYPE 
             8            133 
$`MMP1 MUTATED`
TCGA-D3-A51F TCGA-D9-A6EC TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20H 
       55.73        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 
      126.81        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        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 
       63.78        72.07        64.64         2.60        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  MMP1 MUTATED MMP1 WILD-TYPE 
         20.91           0.16 
  MMP1 MUTATED MMP1 WILD-TYPE 
        168.26         357.37 
  MMP1 MUTATED MMP1 WILD-TYPE 
         60.99          51.12 
[1] "20.9 - 168.3 (61.0)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "1"  
D65V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MMP1 MUTATED                    3             1
  MMP1 WILD-TYPE                 36             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MMP1 MUTATED                                           3                   7
  MMP1 WILD-TYPE                                        57                 164
D65V4, multiclass
                                           clus
vv                                          MMP1 MUTATED MMP1 WILD-TYPE
  DISTANT METASTASIS                                   3             36
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             57
  REGIONAL LYMPH NODE                                  7            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
  MMP1 MUTATED             0       2       2        2        0        2
  MMP1 WILD-TYPE          10       4      22        8       24       14
                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        31         12         23
                vv
clus             STAGE IIIC STAGE IV
  MMP1 MUTATED            1        1
  MMP1 WILD-TYPE         45       15
D65V5, multiclass
             clus
vv            MMP1 MUTATED MMP1 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                2              4
  STAGE I                2             22
  STAGE IA               2              8
  STAGE IB               0             24
  STAGE II               2             14
  STAGE IIA              0             10
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              1             31
  STAGE IIIA             1             12
  STAGE IIIB             0             23
  STAGE IIIC             1             45
  STAGE IV               1             15
[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    50 57 50 55
D65V6, multiclass
       clus
vv      MMP1 MUTATED MMP1 WILD-TYPE
  T0+T1            2             50
  T2               2             57
  T3               4             50
  T4               2             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
  MMP1 MUTATED    11   2   1   0
  MMP1 WILD-TYPE 128  46  32  36
D65V7, multiclass
    clus
vv   MMP1 MUTATED MMP1 WILD-TYPE
  N0           11            128
  N1            2             46
  N2            1             32
  N3            0             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              M0  M1 M1A M1B M1C
  MMP1 MUTATED    13   1   0   0   0
  MMP1 WILD-TYPE 231   3   3   2   8
D65V8, multiclass
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  M0            13            231
  M1             1              3
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 95 67
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      8    1
  MMP1 WILD-TYPE   95   67
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  NO             8             95
  YES            1             67
[1] 2 2
[1] FALSE
D65V10, binary
                cls
clus               0   1
  MMP1 MUTATED     1  13
  MMP1 WILD-TYPE  35 226
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      1   13
  MMP1 WILD-TYPE   35  226
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  NO             1             35
  YES           13            226
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, binary
                cls
clus               0   1
  MMP1 MUTATED     4  10
  MMP1 WILD-TYPE 102 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      4   10
  MMP1 WILD-TYPE  102  160
        clus
vv       MMP1 MUTATED MMP1 WILD-TYPE
  FEMALE            4            102
  MALE             10            160
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP1 MUTATED       0                         0    14
  MMP1 WILD-TYPE     3                         1   258
D65V13, multiclass
                           clus
vv                          MMP1 MUTATED MMP1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               14            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"
D65V14, binary
                cls
clus               0   1
  MMP1 MUTATED     0  13
  MMP1 WILD-TYPE   3 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      0   13
  MMP1 WILD-TYPE    3  256
                        clus
vv                       MMP1 MUTATED MMP1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13            256
[1] 2 2
[1] FALSE

Clustering(66) Variable = KLF11 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  KLF11 MUTATED     5   4
  KLF11 WILD-TYPE 121 136
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             257 
  KLF11 MUTATED KLF11 WILD-TYPE 
              4             136 
$`KLF11 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29L 
       70.16        45.83        44.19         8.12        12.20         1.08 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 
        0.99        44.28        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        86.76        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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
       10.55         6.31         1.12         1.35         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.85        11.61        31.33        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  KLF11 MUTATED KLF11 WILD-TYPE 
           0.99            0.13 
  KLF11 MUTATED KLF11 WILD-TYPE 
          84.72          125.65 
  KLF11 MUTATED KLF11 WILD-TYPE 
          44.19           16.47 
[1] "1.0 - 84.7 (44.2)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.4"
D66V2, survival
                 sevent
clus2               0   1
  KLF11 MUTATED     5   4
  KLF11 WILD-TYPE 124 137
  KLF11 MUTATED KLF11 WILD-TYPE 
              9             261 
  KLF11 MUTATED KLF11 WILD-TYPE 
              4             137 
$`KLF11 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29L 
       71.80        90.90        62.07        94.98        26.89         2.60 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A265 
       22.92       139.89        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        86.76        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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        63.78        72.07        64.64        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  KLF11 MUTATED KLF11 WILD-TYPE 
           2.60            0.16 
  KLF11 MUTATED KLF11 WILD-TYPE 
         139.89          357.37 
  KLF11 MUTATED KLF11 WILD-TYPE 
          71.80           51.35 
[1] "2.6 - 139.9 (71.8)" "0.2 - 357.4 (51.4)"
[1] "hr=" "1.1"
D66V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  KLF11 MUTATED                    2             0
  KLF11 WILD-TYPE                 37             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KLF11 MUTATED                                           2                   5
  KLF11 WILD-TYPE                                        58                 166
D66V4, multiclass
                                           clus
vv                                          KLF11 MUTATED KLF11 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   5             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
  KLF11 MUTATED             0       1       0        1        1        0
  KLF11 WILD-TYPE          10       5      24        9       23       16
                 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        29         13         23
                 vv
clus              STAGE IIIC STAGE IV
  KLF11 MUTATED            1        0
  KLF11 WILD-TYPE         45       16
D66V5, multiclass
             clus
vv            KLF11 MUTATED KLF11 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 0              24
  STAGE IA                1               9
  STAGE IB                1              23
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               3              29
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    51 58 54 54
D66V6, multiclass
       clus
vv      KLF11 MUTATED KLF11 WILD-TYPE
  T0+T1             1              51
  T2                1              58
  T3                0              54
  T4                3              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
  KLF11 MUTATED     4   1   1   1
  KLF11 WILD-TYPE 135  47  32  35
D66V7, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  N0             4             135
  N1             1              47
  N2             1              32
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  KLF11 MUTATED     7   0   0   0   0
  KLF11 WILD-TYPE 237   4   3   2   8
D66V8, multiclass
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  M0              7             237
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 100  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      3    1
  KLF11 WILD-TYPE  100   67
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  NO              3             100
  YES             1              67
[1] 2 2
[1] FALSE
D66V10, binary
                 cls
clus                0   1
  KLF11 MUTATED     1   8
  KLF11 WILD-TYPE  35 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      1    8
  KLF11 WILD-TYPE   35  231
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  NO              1              35
  YES             8             231
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, binary
                 cls
clus                0   1
  KLF11 MUTATED     1   8
  KLF11 WILD-TYPE 105 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      1    8
  KLF11 WILD-TYPE  105  162
        clus
vv       KLF11 MUTATED KLF11 WILD-TYPE
  FEMALE             1             105
  MALE               8             162
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLF11 MUTATED       0                         0     9
  KLF11 WILD-TYPE     3                         1   263
D66V13, multiclass
                           clus
vv                          KLF11 MUTATED KLF11 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                 cls
clus                0   1
  KLF11 MUTATED     0   9
  KLF11 WILD-TYPE   3 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      0    9
  KLF11 WILD-TYPE    3  260
                        clus
vv                       KLF11 MUTATED KLF11 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             260
[1] 2 2
[1] FALSE

Clustering(67) Variable = USP9X MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  USP9X MUTATED     7   6
  USP9X WILD-TYPE 119 134
  USP9X MUTATED USP9X WILD-TYPE 
             13             253 
  USP9X MUTATED USP9X WILD-TYPE 
              6             134 
$`USP9X MUTATED`
TCGA-D3-A3C7 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A2MF TCGA-EE-A2MR TCGA-EE-A3AF 
       46.98        13.22        48.79         2.73        60.49        13.81 
TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A2NH TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F5 
       21.60        38.40        11.74        23.80        12.89        28.73 
TCGA-FW-A3R5 
        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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       125.65       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        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
      124.31       122.73        51.62         3.68        30.15        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        33.60        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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        17.72        78.44        11.80         1.87         1.51 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        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-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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  USP9X MUTATED USP9X WILD-TYPE 
           0.99            0.13 
  USP9X MUTATED USP9X WILD-TYPE 
          60.49          125.65 
  USP9X MUTATED USP9X WILD-TYPE 
          21.60           16.47 
[1] "1.0 - 60.5 (21.6)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.2"
D67V2, survival
                 sevent
clus2               0   1
  USP9X MUTATED     8   6
  USP9X WILD-TYPE 121 135
  USP9X MUTATED USP9X WILD-TYPE 
             14             256 
  USP9X MUTATED USP9X WILD-TYPE 
              6             135 
$`USP9X MUTATED`
TCGA-D3-A3C7 TCGA-D9-A148 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A2MF TCGA-EE-A2MR 
       46.98       151.53        66.25        48.89       268.73       134.40 
TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A198 TCGA-ER-A2NH TCGA-FS-A1Z0 TCGA-FS-A1ZK 
       13.81        64.08        50.76        32.05       202.65        23.93 
TCGA-FS-A4F5 TCGA-FW-A3R5 
       28.73        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      178.32        18.18       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        22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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 
      158.63       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 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      109.58       148.08        31.40        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.72       216.92        48.59       228.59        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-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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  USP9X MUTATED USP9X WILD-TYPE 
          13.81            0.16 
  USP9X MUTATED USP9X WILD-TYPE 
         268.73          357.37 
  USP9X MUTATED USP9X WILD-TYPE 
         49.825          52.585 
[1] "13.8 - 268.7 (49.8)" "0.2 - 357.4 (52.6)" 
[1] "hr=" "1.5"
D67V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  USP9X MUTATED                    2             1
  USP9X WILD-TYPE                 37             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  USP9X MUTATED                                           4                   8
  USP9X WILD-TYPE                                        56                 163
D67V4, multiclass
                                           clus
vv                                          USP9X MUTATED USP9X WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              56
  REGIONAL LYMPH NODE                                   8             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       3        1        1        1
  USP9X WILD-TYPE          10       5      21        9       23       15
                 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        30         12         22
                 vv
clus              STAGE IIIC STAGE IV
  USP9X MUTATED            2        0
  USP9X WILD-TYPE         44       16
D67V5, multiclass
             clus
vv            USP9X MUTATED USP9X WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 3              21
  STAGE IA                1               9
  STAGE IB                1              23
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              1              12
  STAGE IIIB              1              22
  STAGE IIIC              2              44
  STAGE IV                0              16
[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  4  1  2
  USP9X WILD-TYPE    48 55 53 55
D67V6, multiclass
       clus
vv      USP9X MUTATED USP9X WILD-TYPE
  T0+T1             4              48
  T2                4              55
  T3                1              53
  T4                2              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
  USP9X MUTATED     7   2   2   3
  USP9X WILD-TYPE 132  46  31  33
D67V7, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  N0             7             132
  N1             2              46
  N2             2              31
  N3             3              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
  USP9X MUTATED    14   0   0   1   0
  USP9X WILD-TYPE 230   4   3   1   8
D67V8, multiclass
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  M0             14             230
  M1              0               4
  M1A             0               3
  M1B             1               1
  M1C             0               8
[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 97 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      6    2
  USP9X WILD-TYPE   97   66
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO              6              97
  YES             2              66
[1] 2 2
[1] FALSE
D67V10, binary
                 cls
clus                0   1
  USP9X MUTATED     3  12
  USP9X WILD-TYPE  33 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      3   12
  USP9X WILD-TYPE   33  227
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO              3              33
  YES            12             227
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, binary
                 cls
clus                0   1
  USP9X MUTATED     7   8
  USP9X WILD-TYPE  99 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      7    8
  USP9X WILD-TYPE   99  162
        clus
vv       USP9X MUTATED USP9X WILD-TYPE
  FEMALE             7              99
  MALE               8             162
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP9X MUTATED       0                         0    15
  USP9X WILD-TYPE     3                         1   257
D67V13, multiclass
                           clus
vv                          USP9X MUTATED USP9X WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                15             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"
D67V14, binary
                 cls
clus                0   1
  USP9X MUTATED     0  15
  USP9X WILD-TYPE   3 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      0   15
  USP9X WILD-TYPE    3  254
                        clus
vv                       USP9X MUTATED USP9X WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            15             254
[1] 2 2
[1] FALSE

Clustering(68) Variable = PTK7 MUTATION ANALYSIS
D68V1, survival
                sevent
clus2              0   1
  PTK7 MUTATED     8   8
  PTK7 WILD-TYPE 118 132
  PTK7 MUTATED PTK7 WILD-TYPE 
            16            250 
  PTK7 MUTATED PTK7 WILD-TYPE 
             8            132 
$`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        62.79 
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 TCGA-GF-A6C9 
        5.23         2.27         0.99        11.61 

$`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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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-A29A 
        4.31        60.23         4.34        15.85         9.21         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        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62        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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        18.41        21.73        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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-A42K TCGA-FR-A44A 
       11.74         9.04         6.58        22.49         5.62        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-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        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  PTK7 MUTATED PTK7 WILD-TYPE 
          0.99           0.13 
  PTK7 MUTATED PTK7 WILD-TYPE 
        124.31         125.65 
  PTK7 MUTATED PTK7 WILD-TYPE 
         9.995         17.640 
[1] "1.0 - 124.3 (10.0)" "0.1 - 125.7 (17.6)"
[1] "hr=" "1.3"
D68V2, survival
                sevent
clus2              0   1
  PTK7 MUTATED     8   8
  PTK7 WILD-TYPE 121 133
  PTK7 MUTATED PTK7 WILD-TYPE 
            16            254 
  PTK7 MUTATED PTK7 WILD-TYPE 
             8            133 
$`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        63.78 
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 TCGA-GF-A6C9 
       27.02        77.88        22.92        11.74 

$`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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56       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        64.64         2.60        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      162.48        71.21        53.26       122.73        51.62        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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58        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-A19P 
      268.93       152.35         6.44       131.51        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       80.32        46.98         6.77       174.21        15.72       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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45         0.20        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  PTK7 MUTATED PTK7 WILD-TYPE 
          3.68           0.16 
  PTK7 MUTATED PTK7 WILD-TYPE 
        148.08         357.37 
  PTK7 MUTATED PTK7 WILD-TYPE 
        57.485         51.485 
[1] "3.7 - 148.1 (57.5)" "0.2 - 357.4 (51.5)"
[1] "hr=" "1.2"
D68V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  PTK7 MUTATED                    2             1
  PTK7 WILD-TYPE                 37             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PTK7 MUTATED                                           4                  10
  PTK7 WILD-TYPE                                        56                 161
D68V4, multiclass
                                           clus
vv                                          PTK7 MUTATED PTK7 WILD-TYPE
  DISTANT METASTASIS                                   2             37
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             56
  REGIONAL LYMPH NODE                                 10            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
  PTK7 MUTATED             0       1       1        0        3        1
  PTK7 WILD-TYPE          10       5      23       10       21       15
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PTK7 MUTATED           0         1         0         3          1          2
  PTK7 WILD-TYPE        10        13         9        29         12         21
                vv
clus             STAGE IIIC STAGE IV
  PTK7 MUTATED            2        2
  PTK7 WILD-TYPE         44       14
D68V5, multiclass
             clus
vv            PTK7 MUTATED PTK7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                1             23
  STAGE IA               0             10
  STAGE IB               3             21
  STAGE II               1             15
  STAGE IIA              0             10
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              3             29
  STAGE IIIA             1             12
  STAGE IIIB             2             21
  STAGE IIIC             2             44
  STAGE IV               2             14
[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    50 54 49 56
D68V6, multiclass
       clus
vv      PTK7 MUTATED PTK7 WILD-TYPE
  T0+T1            2             50
  T2               5             54
  T3               5             49
  T4               1             56
[1] 4 2
[1] TRUE
[1] "dimension of 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   3   2   2
  PTK7 WILD-TYPE 130  45  31  34
D68V7, multiclass
    clus
vv   PTK7 MUTATED PTK7 WILD-TYPE
  N0            9            130
  N1            3             45
  N2            2             31
  N3            2             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  PTK7 MUTATED    14   0   1   0   1
  PTK7 WILD-TYPE 230   4   2   2   7
D68V8, multiclass
     clus
vv    PTK7 MUTATED PTK7 WILD-TYPE
  M0            14            230
  M1             0              4
  M1A            1              2
  M1B            0              2
  M1C            1              7
[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 97 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      6    4
  PTK7 WILD-TYPE   97   64
     clus
vv    PTK7 MUTATED PTK7 WILD-TYPE
  NO             6             97
  YES            4             64
[1] 2 2
[1] FALSE
D68V10, binary
                cls
clus               0   1
  PTK7 MUTATED     3  14
  PTK7 WILD-TYPE  33 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      3   14
  PTK7 WILD-TYPE   33  225
     clus
vv    PTK7 MUTATED PTK7 WILD-TYPE
  NO             3             33
  YES           14            225
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, binary
                cls
clus               0   1
  PTK7 MUTATED     4  13
  PTK7 WILD-TYPE 102 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      4   13
  PTK7 WILD-TYPE  102  157
        clus
vv       PTK7 MUTATED PTK7 WILD-TYPE
  FEMALE            4            102
  MALE             13            157
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTK7 MUTATED       0                         0    17
  PTK7 WILD-TYPE     3                         1   255
D68V13, multiclass
                           clus
vv                          PTK7 MUTATED PTK7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               17            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"
D68V14, binary
                cls
clus               0   1
  PTK7 MUTATED     1  16
  PTK7 WILD-TYPE   2 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK7 MUTATED      1   16
  PTK7 WILD-TYPE    2  253
                        clus
vv                       PTK7 MUTATED PTK7 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           16            253
[1] 2 2
[1] FALSE

Clustering(69) Variable = SLC14A1 MUTATION ANALYSIS
D69V1, survival
                   sevent
clus2                 0   1
  SLC14A1 MUTATED     7  11
  SLC14A1 WILD-TYPE 119 129
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               18               248 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               11               129 
$`SLC14A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A51T TCGA-D3-A5GO TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A20C 
       70.16        25.78        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        62.79         1.08        36.30 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MF TCGA-EE-A3AC TCGA-ER-A19P TCGA-FW-A3R5 
        1.15         8.84         2.73        51.62        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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       32.28        21.44        32.61        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        19.00        13.35        13.22        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-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
       60.23        15.85         1.18         9.90        37.97         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85        39.62         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        32.15         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        36.33        51.12        34.29        17.98        60.00 
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        55.69         5.42        13.02        34.98        36.33 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       124.31       122.73         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
             0.99              0.13 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
            70.16            125.65 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
           11.360            17.525 
[1] "1.0 - 70.2 (11.4)"  "0.1 - 125.7 (17.5)"
[1] "hr=" "1.4"
D69V2, survival
                   sevent
clus2                 0   1
  SLC14A1 MUTATED     7  11
  SLC14A1 WILD-TYPE 122 130
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               18               252 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
               11               130 
$`SLC14A1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A51T TCGA-D3-A5GO TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A20C 
       71.80        26.89       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        63.78         2.60        36.82 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MF TCGA-EE-A3AC TCGA-ER-A19P TCGA-FW-A3R5 
       14.30        21.67       268.73        51.62       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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62        63.81       135.75       178.32        18.18 
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 
       22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       17.29        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       133.81        91.56 
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        64.64        56.84 
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 
      195.02        17.92        46.82       102.90        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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       158.63       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       134.40       162.48        71.21        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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
             2.60              0.16 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
           268.73            357.37 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
           57.485            51.680 
[1] "2.6 - 268.7 (57.5)" "0.2 - 357.4 (51.7)"
[1] "hr=" "1"  
D69V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC14A1 MUTATED                    4             0
  SLC14A1 WILD-TYPE                 35             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC14A1 MUTATED                                           2
  SLC14A1 WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  SLC14A1 MUTATED                    12
  SLC14A1 WILD-TYPE                 159
D69V4, multiclass
                                           clus
vv                                          SLC14A1 MUTATED SLC14A1 WILD-TYPE
  DISTANT METASTASIS                                      4                35
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                58
  REGIONAL LYMPH NODE                                    12               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       3        1        0        2
  SLC14A1 WILD-TYPE          10       5      21        9       24       14
                   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        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC14A1 MUTATED            1          5        0
  SLC14A1 WILD-TYPE         22         41       16
D69V5, multiclass
             clus
vv            SLC14A1 MUTATED SLC14A1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   3                21
  STAGE IA                  1                 9
  STAGE IB                  0                24
  STAGE II                  2                14
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 3                29
  STAGE IIIA                1                12
  STAGE IIIB                1                22
  STAGE IIIC                5                41
  STAGE IV                  0                16
[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  3  3  6
  SLC14A1 WILD-TYPE    49 56 51 51
D69V6, multiclass
       clus
vv      SLC14A1 MUTATED SLC14A1 WILD-TYPE
  T0+T1               3                49
  T2                  3                56
  T3                  3                51
  T4                  6                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
  SLC14A1 MUTATED     8   6   2   2
  SLC14A1 WILD-TYPE 131  42  31  34
D69V7, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  N0               8               131
  N1               6                42
  N2               2                31
  N3               2                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  SLC14A1 MUTATED    18   0   0   0   0
  SLC14A1 WILD-TYPE 226   4   3   2   8
D69V8, multiclass
     clus
vv    SLC14A1 MUTATED SLC14A1 WILD-TYPE
  M0               18               226
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 99 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      4    4
  SLC14A1 WILD-TYPE   99   64
     clus
vv    SLC14A1 MUTATED SLC14A1 WILD-TYPE
  NO                4                99
  YES               4                64
[1] 2 2
[1] FALSE
D69V10, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     1  17
  SLC14A1 WILD-TYPE  35 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      1   17
  SLC14A1 WILD-TYPE   35  222
     clus
vv    SLC14A1 MUTATED SLC14A1 WILD-TYPE
  NO                1                35
  YES              17               222
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     3  15
  SLC14A1 WILD-TYPE 103 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      3   15
  SLC14A1 WILD-TYPE  103  155
        clus
vv       SLC14A1 MUTATED SLC14A1 WILD-TYPE
  FEMALE               3               103
  MALE                15               155
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC14A1 MUTATED       0                         0    18
  SLC14A1 WILD-TYPE     3                         1   254
D69V13, multiclass
                           clus
vv                          SLC14A1 MUTATED SLC14A1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  18               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"
D69V14, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     0  16
  SLC14A1 WILD-TYPE   3 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      0   16
  SLC14A1 WILD-TYPE    3  253
                        clus
vv                       SLC14A1 MUTATED SLC14A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              16               253
[1] 2 2
[1] FALSE

Clustering(70) Variable = PROX2 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  PROX2 MUTATED     7   5
  PROX2 WILD-TYPE 119 135
  PROX2 MUTATED PROX2 WILD-TYPE 
             12             254 
  PROX2 MUTATED PROX2 WILD-TYPE 
              5             135 
$`PROX2 MUTATED`
TCGA-D3-A51R TCGA-DA-A1IC TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2MT TCGA-EE-A3AB 
       32.61         6.64        62.79        39.62        52.67       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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       54.31        32.28        21.44        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55        36.85         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-A2A0 
        8.84         9.99         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16         5.56 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31        51.62         3.68        30.15        13.81        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
        3.22        22.92        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       13.45        28.60        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         7.36        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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  PROX2 MUTATED PROX2 WILD-TYPE 
           0.99            0.13 
  PROX2 MUTATED PROX2 WILD-TYPE 
         122.73          125.65 
  PROX2 MUTATED PROX2 WILD-TYPE 
          30.67           16.19 
[1] "1.0 - 122.7 (30.7)" "0.1 - 125.7 (16.2)"
[1] "hr=" "1.6"
D70V2, survival
                 sevent
clus2               0   1
  PROX2 MUTATED     7   5
  PROX2 WILD-TYPE 122 136
  PROX2 MUTATED PROX2 WILD-TYPE 
             12             258 
  PROX2 MUTATED PROX2 WILD-TYPE 
              5             136 
$`PROX2 MUTATED`
TCGA-D3-A51R TCGA-DA-A1IC TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2MT TCGA-EE-A3AB 
       63.81        68.09        63.78        56.84        71.21       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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        32.94        22.62        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        64.64 
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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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-A3AC 
       43.23       134.40       162.48        53.26       124.31        51.62 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  PROX2 MUTATED PROX2 WILD-TYPE 
          20.91            0.16 
  PROX2 MUTATED PROX2 WILD-TYPE 
         122.73          357.37 
  PROX2 MUTATED PROX2 WILD-TYPE 
         50.445          51.815 
[1] "20.9 - 122.7 (50.4)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1"  
D70V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PROX2 MUTATED                    2             0
  PROX2 WILD-TYPE                 37             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PROX2 MUTATED                                           4                   7
  PROX2 WILD-TYPE                                        56                 164
D70V4, multiclass
                                           clus
vv                                          PROX2 MUTATED PROX2 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              56
  REGIONAL LYMPH NODE                                   7             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
  PROX2 MUTATED             1       0       0        0        3        0
  PROX2 WILD-TYPE           9       6      24       10       21       16
                 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        28         13         21
                 vv
clus              STAGE IIIC STAGE IV
  PROX2 MUTATED            0        1
  PROX2 WILD-TYPE         46       15
D70V5, multiclass
             clus
vv            PROX2 MUTATED PROX2 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                3              21
  STAGE II                0              16
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               4              28
  STAGE IIIA              0              13
  STAGE IIIB              2              21
  STAGE IIIC              0              46
  STAGE IV                1              15
[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    50 55 51 56
D70V6, multiclass
       clus
vv      PROX2 MUTATED PROX2 WILD-TYPE
  T0+T1             2              50
  T2                4              55
  T3                3              51
  T4                1              56
[1] 4 2
[1] TRUE
[1] "dimension of 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 133  46  29  36
D70V7, multiclass
    clus
vv   PROX2 MUTATED PROX2 WILD-TYPE
  N0             6             133
  N1             2              46
  N2             4              29
  N3             0              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               M0  M1 M1A M1B M1C
  PROX2 MUTATED    11   1   0   0   0
  PROX2 WILD-TYPE 233   3   3   2   8
D70V8, multiclass
     clus
vv    PROX2 MUTATED PROX2 WILD-TYPE
  M0             11             233
  M1              1               3
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 96 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      7    0
  PROX2 WILD-TYPE   96   68
     clus
vv    PROX2 MUTATED PROX2 WILD-TYPE
  NO              7              96
  YES             0              68
[1] 2 2
[1] FALSE
D70V10, binary
                 cls
clus                0   1
  PROX2 MUTATED     4   9
  PROX2 WILD-TYPE  32 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      4    9
  PROX2 WILD-TYPE   32  230
     clus
vv    PROX2 MUTATED PROX2 WILD-TYPE
  NO              4              32
  YES             9             230
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, binary
                 cls
clus                0   1
  PROX2 MUTATED     4   9
  PROX2 WILD-TYPE 102 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      4    9
  PROX2 WILD-TYPE  102  161
        clus
vv       PROX2 MUTATED PROX2 WILD-TYPE
  FEMALE             4             102
  MALE               9             161
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PROX2 MUTATED       0                         0    13
  PROX2 WILD-TYPE     3                         1   259
D70V13, multiclass
                           clus
vv                          PROX2 MUTATED PROX2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             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"
D70V14, binary
                 cls
clus                0   1
  PROX2 MUTATED     0  13
  PROX2 WILD-TYPE   3 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX2 MUTATED      0   13
  PROX2 WILD-TYPE    3  256
                        clus
vv                       PROX2 MUTATED PROX2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             256
[1] 2 2
[1] FALSE

Clustering(71) Variable = DNMBP MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2               0   1
  DNMBP MUTATED     9  10
  DNMBP WILD-TYPE 117 130
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             247 
  DNMBP MUTATED DNMBP WILD-TYPE 
             10             130 
$`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        23.15        11.15        62.79 
TCGA-EE-A29Q TCGA-EE-A2A6 TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS 
        8.09        36.33         1.15        63.42        60.49        53.16 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A193 TCGA-FS-A1ZP TCGA-FW-A3R5 
       51.62        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        86.76        44.19 
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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.20        19.00        13.35        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        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        7.99         9.90        37.97         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       39.62         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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69 
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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56       125.65       111.91        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        52.67         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-A3JB TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       10.13        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  DNMBP MUTATED DNMBP WILD-TYPE 
           0.99            0.13 
  DNMBP MUTATED DNMBP WILD-TYPE 
         103.59          125.65 
  DNMBP MUTATED DNMBP WILD-TYPE 
          31.40           16.01 
[1] "1.0 - 103.6 (31.4)" "0.1 - 125.7 (16.0)"
[1] "hr=" "1.2"
D71V2, survival
                 sevent
clus2               0   1
  DNMBP MUTATED     9  10
  DNMBP WILD-TYPE 120 131
  DNMBP MUTATED DNMBP WILD-TYPE 
             19             251 
  DNMBP MUTATED DNMBP WILD-TYPE 
             10             131 
$`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        68.25        13.97        63.78 
TCGA-EE-A29Q TCGA-EE-A2A6 TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS 
       37.35        86.14        14.30        96.23       134.40       162.48 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A193 TCGA-FS-A1ZP TCGA-FW-A3R5 
       51.62        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        86.76        62.07 
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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       137.92       178.32        18.18 
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 
       22.29         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        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        39.29        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       43.23        71.21        53.26       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32       201.80        27.35        51.35       109.58 
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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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-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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       11.74       139.89       117.93        84.72        10.13        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  DNMBP MUTATED DNMBP WILD-TYPE 
          11.87            0.16 
  DNMBP MUTATED DNMBP WILD-TYPE 
         162.48          357.37 
  DNMBP MUTATED DNMBP WILD-TYPE 
          63.78           50.89 
[1] "11.9 - 162.5 (63.8)" "0.2 - 357.4 (50.9)" 
[1] "hr=" "1.1"
D71V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DNMBP MUTATED                    0             0
  DNMBP WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DNMBP MUTATED                                           4                  15
  DNMBP WILD-TYPE                                        56                 156
D71V4, multiclass
                                           clus
vv                                          DNMBP MUTATED DNMBP WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              56
  REGIONAL LYMPH NODE                                  15             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
  DNMBP MUTATED             0       0       2        1        1        3
  DNMBP WILD-TYPE          10       6      22        9       23       13
                 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        27         12         22
                 vv
clus              STAGE IIIC STAGE IV
  DNMBP MUTATED            2        0
  DNMBP WILD-TYPE         44       16
D71V5, multiclass
             clus
vv            DNMBP MUTATED DNMBP WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              22
  STAGE IA                1               9
  STAGE IB                1              23
  STAGE II                3              13
  STAGE IIA               0              10
  STAGE IIB               2              12
  STAGE IIC               0               9
  STAGE III               5              27
  STAGE IIIA              1              12
  STAGE IIIB              1              22
  STAGE IIIC              2              44
  STAGE IV                0              16
[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    47 57 48 53
D71V6, multiclass
       clus
vv      DNMBP MUTATED DNMBP WILD-TYPE
  T0+T1             5              47
  T2                2              57
  T3                6              48
  T4                4              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
  DNMBP MUTATED    10   5   3   0
  DNMBP WILD-TYPE 129  43  30  36
D71V7, multiclass
    clus
vv   DNMBP MUTATED DNMBP WILD-TYPE
  N0            10             129
  N1             5              43
  N2             3              30
  N3             0              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               M0  M1 M1A M1B M1C
  DNMBP MUTATED    18   0   0   0   0
  DNMBP WILD-TYPE 226   4   3   2   8
D71V8, multiclass
     clus
vv    DNMBP MUTATED DNMBP WILD-TYPE
  M0             18             226
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 94 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      9    3
  DNMBP WILD-TYPE   94   65
     clus
vv    DNMBP MUTATED DNMBP WILD-TYPE
  NO              9              94
  YES             3              65
[1] 2 2
[1] FALSE
D71V10, binary
                 cls
clus                0   1
  DNMBP MUTATED     3  16
  DNMBP WILD-TYPE  33 223
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      3   16
  DNMBP WILD-TYPE   33  223
     clus
vv    DNMBP MUTATED DNMBP WILD-TYPE
  NO              3              33
  YES            16             223
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, binary
                 cls
clus                0   1
  DNMBP MUTATED     3  16
  DNMBP WILD-TYPE 103 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      3   16
  DNMBP WILD-TYPE  103  154
        clus
vv       DNMBP MUTATED DNMBP WILD-TYPE
  FEMALE             3             103
  MALE              16             154
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNMBP MUTATED       0                         0    19
  DNMBP WILD-TYPE     3                         1   253
D71V13, multiclass
                           clus
vv                          DNMBP MUTATED DNMBP WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                19             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"
D71V14, binary
                 cls
clus                0   1
  DNMBP MUTATED     0  19
  DNMBP WILD-TYPE   3 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMBP MUTATED      0   19
  DNMBP WILD-TYPE    3  250
                        clus
vv                       DNMBP MUTATED DNMBP WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            19             250
[1] 2 2
[1] FALSE

Clustering(72) Variable = MPP7 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2              0   1
  MPP7 MUTATED    15  14
  MPP7 WILD-TYPE 111 126
  MPP7 MUTATED MPP7 WILD-TYPE 
            29            237 
  MPP7 MUTATED MPP7 WILD-TYPE 
            14            126 
$`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        17.72        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 
       62.79        34.29        36.33        60.49        53.16        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        86.76        11.41        44.19         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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       32.61        25.78        52.01        47.87        13.68        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
        4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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-A20F TCGA-EE-A20H 
       12.20         5.13         4.31        60.23        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        1.18         9.90         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        17.98        60.00        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        55.69 
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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
       56.02        25.08        26.99        21.60        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22         0.95        18.41        21.73        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-A19G TCGA-ER-A19H TCGA-ER-A19L 
        3.78         3.52        11.90       114.15        34.88        13.45 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       28.60        34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         7.30        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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       14.20         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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       44.28        31.33        84.72        10.13        16.24        12.16 
TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       14.70         0.33         0.69 

  MPP7 MUTATED MPP7 WILD-TYPE 
          0.99           0.13 
  MPP7 MUTATED MPP7 WILD-TYPE 
         62.79         125.65 
  MPP7 MUTATED MPP7 WILD-TYPE 
         14.24          17.56 
[1] "1.0 - 62.8 (14.2)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1"  
D72V2, survival
                sevent
clus2              0   1
  MPP7 MUTATED    16  14
  MPP7 WILD-TYPE 113 127
  MPP7 MUTATED MPP7 WILD-TYPE 
            30            240 
  MPP7 MUTATED MPP7 WILD-TYPE 
            14            127 
$`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        18.18        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        63.78        67.43        94.82       134.40       162.48 
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        86.76        11.87        62.07       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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       63.81        26.89       135.75       137.92       178.32       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81        91.56       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 
       64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        36.82        39.29        86.14        59.28       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58       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-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      268.93       152.35       131.51        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-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-A4FB TCGA-FS-A4FC 
       77.82        66.67        28.73       174.84        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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       10.13        64.44        32.48        39.58         0.33         0.69 

  MPP7 MUTATED MPP7 WILD-TYPE 
          6.44           0.16 
  MPP7 MUTATED MPP7 WILD-TYPE 
        194.83         357.37 
  MPP7 MUTATED MPP7 WILD-TYPE 
        48.345         52.585 
[1] "6.4 - 194.8 (48.3)" "0.2 - 357.4 (52.6)"
[1] "hr=" "1.1"
D72V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MPP7 MUTATED                    6             1
  MPP7 WILD-TYPE                 33             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MPP7 MUTATED                                           4                  19
  MPP7 WILD-TYPE                                        56                 152
D72V4, multiclass
                                           clus
vv                                          MPP7 MUTATED MPP7 WILD-TYPE
  DISTANT METASTASIS                                   6             33
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             56
  REGIONAL LYMPH NODE                                 19            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
  MPP7 MUTATED             0       1       1        1        5        2
  MPP7 WILD-TYPE          10       5      23        9       19       14
                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        30         11         21
                vv
clus             STAGE IIIC STAGE IV
  MPP7 MUTATED            5        3
  MPP7 WILD-TYPE         41       13
D72V5, multiclass
             clus
vv            MPP7 MUTATED MPP7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                1              5
  STAGE I                1             23
  STAGE IA               1              9
  STAGE IB               5             19
  STAGE II               2             14
  STAGE IIA              0             10
  STAGE IIB              3             11
  STAGE IIC              0              9
  STAGE III              2             30
  STAGE IIIA             2             11
  STAGE IIIB             2             21
  STAGE IIIC             5             41
  STAGE IV               3             13
[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    47 54 45 54
D72V6, multiclass
       clus
vv      MPP7 MUTATED MPP7 WILD-TYPE
  T0+T1            5             47
  T2               5             54
  T3               9             45
  T4               3             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
  MPP7 MUTATED    15   7   3   4
  MPP7 WILD-TYPE 124  41  30  32
D72V7, multiclass
    clus
vv   MPP7 MUTATED MPP7 WILD-TYPE
  N0           15            124
  N1            7             41
  N2            3             30
  N3            4             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
  MPP7 MUTATED    26   2   0   0   1
  MPP7 WILD-TYPE 218   2   3   2   7
D72V8, multiclass
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  M0            26            218
  M1             2              2
  M1A            0              3
  M1B            0              2
  M1C            1              7
[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 86 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED     17    4
  MPP7 WILD-TYPE   86   64
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO            17             86
  YES            4             64
[1] 2 2
[1] FALSE
D72V10, binary
                cls
clus               0   1
  MPP7 MUTATED     6  24
  MPP7 WILD-TYPE  30 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      6   24
  MPP7 WILD-TYPE   30  215
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO             6             30
  YES           24            215
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, binary
                cls
clus               0   1
  MPP7 MUTATED     6  24
  MPP7 WILD-TYPE 100 146
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      6   24
  MPP7 WILD-TYPE  100  146
        clus
vv       MPP7 MUTATED MPP7 WILD-TYPE
  FEMALE            6            100
  MALE             24            146
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MPP7 MUTATED       0                         0    30
  MPP7 WILD-TYPE     3                         1   242
D72V13, multiclass
                           clus
vv                          MPP7 MUTATED MPP7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               30            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"
D72V14, binary
                cls
clus               0   1
  MPP7 MUTATED     0  29
  MPP7 WILD-TYPE   3 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      0   29
  MPP7 WILD-TYPE    3  240
                        clus
vv                       MPP7 MUTATED MPP7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           29            240
[1] 2 2
[1] FALSE

Clustering(73) Variable = IFNGR2 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2                0   1
  IFNGR2 MUTATED     1   3
  IFNGR2 WILD-TYPE 125 137
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              262 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               3              137 
$`IFNGR2 MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-EE-A180 TCGA-EE-A29E 
       85.32         8.38         8.12        62.79 

$`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        86.76        11.41        44.19         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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       11.57        10.55         6.31         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        60.23         4.34        15.85         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 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
            8.12             0.13 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
           85.32           125.65 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          35.585           16.900 
[1] "8.1 - 85.3 (35.6)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.2"
D73V2, survival
                  sevent
clus2                0   1
  IFNGR2 MUTATED     1   3
  IFNGR2 WILD-TYPE 128 138
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              266 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               3              138 
$`IFNGR2 MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-EE-A180 TCGA-EE-A29E 
      103.10        65.49        94.98        63.78 

$`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        86.76        11.87        62.07       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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
           63.78             0.16 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          103.10           357.37 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          80.235           51.120 
[1] "63.8 - 103.1 (80.2)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "1.2"
D73V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  IFNGR2 MUTATED                    1             0
  IFNGR2 WILD-TYPE                 38             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  IFNGR2 MUTATED                                           0
  IFNGR2 WILD-TYPE                                        60
                  vv
clus               REGIONAL LYMPH NODE
  IFNGR2 MUTATED                     3
  IFNGR2 WILD-TYPE                 168
D73V4, multiclass
                                           clus
vv                                          IFNGR2 MUTATED IFNGR2 WILD-TYPE
  DISTANT METASTASIS                                     1               38
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              0               60
  REGIONAL LYMPH NODE                                    3              168
[1] 4 2
[1] 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      24       10       23       16
                  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        31         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  IFNGR2 MUTATED            1          1        0
  IFNGR2 WILD-TYPE         22         45       16
D73V5, multiclass
             clus
vv            IFNGR2 MUTATED IFNGR2 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               24
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 0               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               31
  STAGE IIIA               0               13
  STAGE IIIB               1               22
  STAGE IIIC               1               45
  STAGE IV                 0               16
[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    52 58 52 56
D73V6, multiclass
       clus
vv      IFNGR2 MUTATED IFNGR2 WILD-TYPE
  T0+T1              0               52
  T2                 1               58
  T3                 2               52
  T4                 1               56
[1] 4 2
[1] TRUE
[1] "dimension of 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 137  46  33  36
D73V7, multiclass
    clus
vv   IFNGR2 MUTATED IFNGR2 WILD-TYPE
  N0              2              137
  N1              2               46
  N2              0               33
  N3              0               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                M0  M1 M1A M1B M1C
  IFNGR2 MUTATED     4   0   0   0   0
  IFNGR2 WILD-TYPE 240   4   3   2   8
D73V8, multiclass
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  M0               4              240
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 100  67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      3    1
  IFNGR2 WILD-TYPE  100   67
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               3              100
  YES              1               67
[1] 2 2
[1] FALSE
D73V10, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE  36 235
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE   36  235
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               0               36
  YES              4              235
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE 106 166
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE  106  166
        clus
vv       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  FEMALE              0              106
  MALE                4              166
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFNGR2 MUTATED       0                         0     4
  IFNGR2 WILD-TYPE     3                         1   268
D73V13, multiclass
                           clus
vv                          IFNGR2 MUTATED IFNGR2 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  4              268
[1] 3 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   3 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE    3  265
                        clus
vv                       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              265
[1] 2 2
[1] FALSE

Clustering(74) Variable = ASNSD1 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2                0   1
  ASNSD1 MUTATED     3   2
  ASNSD1 WILD-TYPE 123 138
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               5              261 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               2              138 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
       17.72        23.11         4.01        21.93        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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
            1.35             0.13 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           82.29           125.65 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           46.32            16.47 
[1] "1.4 - 82.3 (46.3)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.6"
D74V2, survival
                  sevent
clus2                0   1
  ASNSD1 MUTATED     4   2
  ASNSD1 WILD-TYPE 125 139
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               6              264 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               2              139 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       18.18       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 
       22.29        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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        63.78        72.07        64.64         2.60        56.84 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  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           51.815 
[1] "9.9 - 166.5 (53.9)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.5"
D74V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ASNSD1 MUTATED                    2             1
  ASNSD1 WILD-TYPE                 37             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ASNSD1 MUTATED                                           1
  ASNSD1 WILD-TYPE                                        59
                  vv
clus               REGIONAL LYMPH NODE
  ASNSD1 MUTATED                     3
  ASNSD1 WILD-TYPE                 168
D74V4, multiclass
                                           clus
vv                                          ASNSD1 MUTATED ASNSD1 WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               59
  REGIONAL LYMPH NODE                                    3              168
[1] 4 2
[1] 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      23       10       24       16
                  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        32         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ASNSD1 MUTATED            0          2        0
  ASNSD1 WILD-TYPE         23         44       16
D74V5, multiclass
             clus
vv            ASNSD1 MUTATED ASNSD1 WILD-TYPE
  I OR II NOS              2                8
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 0               10
  STAGE IB                 0               24
  STAGE II                 0               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                0               32
  STAGE IIIA               1               12
  STAGE IIIB               0               23
  STAGE IIIC               2               44
  STAGE IV                 0               16
[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    52 56 53 56
D74V6, multiclass
       clus
vv      ASNSD1 MUTATED ASNSD1 WILD-TYPE
  T0+T1              0               52
  T2                 3               56
  T3                 1               53
  T4                 1               56
[1] 4 2
[1] TRUE
[1] "dimension of 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 136  46  33  34
D74V7, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  N0              3              136
  N1              2               46
  N2              0               33
  N3              2               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ASNSD1 MUTATED     6   0   0   1   0
  ASNSD1 WILD-TYPE 238   4   3   1   8
D74V8, multiclass
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  M0               6              238
  M1               0                4
  M1A              0                3
  M1B              1                1
  M1C              0                8
[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 100  67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      3    1
  ASNSD1 WILD-TYPE  100   67
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  NO               3              100
  YES              1               67
[1] 2 2
[1] FALSE
D74V10, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     0   7
  ASNSD1 WILD-TYPE  36 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      0    7
  ASNSD1 WILD-TYPE   36  232
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  NO               0               36
  YES              7              232
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     4   3
  ASNSD1 WILD-TYPE 102 167
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      4    3
  ASNSD1 WILD-TYPE  102  167
        clus
vv       ASNSD1 MUTATED ASNSD1 WILD-TYPE
  FEMALE              4              102
  MALE                3              167
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASNSD1 MUTATED       0                         0     7
  ASNSD1 WILD-TYPE     3                         1   265
D74V13, multiclass
                           clus
vv                          ASNSD1 MUTATED ASNSD1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  7              265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     0   7
  ASNSD1 WILD-TYPE   3 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      0    7
  ASNSD1 WILD-TYPE    3  262
                        clus
vv                       ASNSD1 MUTATED ASNSD1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7              262
[1] 2 2
[1] FALSE

Clustering(75) Variable = RB1 MUTATION ANALYSIS
D75V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     4   4
  RB1 WILD-TYPE 122 136
  RB1 MUTATED RB1 WILD-TYPE 
            8           258 
  RB1 MUTATED RB1 WILD-TYPE 
            4           136 
$`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        52.67        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        86.76        11.41        44.19         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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        9.21         1.18         7.99        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       85.74        15.72        64.47         3.45        11.01        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.99         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  RB1 MUTATED RB1 WILD-TYPE 
         0.13          0.16 
  RB1 MUTATED RB1 WILD-TYPE 
       110.79        125.65 
  RB1 MUTATED RB1 WILD-TYPE 
       22.700        16.305 
[1] "0.1 - 110.8 (22.7)" "0.2 - 125.7 (16.3)"
[1] "hr=" "1.3"
D75V2, survival
               sevent
clus2             0   1
  RB1 MUTATED     4   4
  RB1 WILD-TYPE 125 137
  RB1 MUTATED RB1 WILD-TYPE 
            8           262 
  RB1 MUTATED RB1 WILD-TYPE 
            4           137 
$`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        71.21        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        86.76        11.87        62.07       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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        10.13        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  RB1 MUTATED RB1 WILD-TYPE 
        36.95          0.16 
  RB1 MUTATED RB1 WILD-TYPE 
       202.65        357.37 
  RB1 MUTATED RB1 WILD-TYPE 
        75.91         51.12 
[1] "37.0 - 202.7 (75.9)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "1.4"
D75V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  RB1 MUTATED                    3             0
  RB1 WILD-TYPE                 36             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RB1 MUTATED                                           2                   4
  RB1 WILD-TYPE                                        58                 167
D75V4, multiclass
                                           clus
vv                                          RB1 MUTATED RB1 WILD-TYPE
  DISTANT METASTASIS                                  3            36
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           2            58
  REGIONAL LYMPH NODE                                 4           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
  RB1 MUTATED             0       1       0        1        2        0
  RB1 WILD-TYPE          10       5      24        9       22       16
               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        30         12         23
               vv
clus            STAGE IIIC STAGE IV
  RB1 MUTATED            0        0
  RB1 WILD-TYPE         46       16
D75V5, multiclass
             clus
vv            RB1 MUTATED RB1 WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               1             5
  STAGE I               0            24
  STAGE IA              1             9
  STAGE IB              2            22
  STAGE II              0            16
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             0             9
  STAGE III             2            30
  STAGE IIIA            1            12
  STAGE IIIB            0            23
  STAGE IIIC            0            46
  STAGE IV              0            16
[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    49 58 53 55
D75V6, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T0+T1           3            49
  T2              1            58
  T3              1            53
  T4              2            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
  RB1 MUTATED     5   2   1   0
  RB1 WILD-TYPE 134  46  32  36
D75V7, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           5           134
  N1           2            46
  N2           1            32
  N3           0            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             M0  M1 M1A M1B M1C
  RB1 MUTATED     8   0   0   0   0
  RB1 WILD-TYPE 236   4   3   2   8
D75V8, multiclass
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  M0            8           236
  M1            0             4
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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 98 67
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      5    1
  RB1 WILD-TYPE   98   67
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            5            98
  YES           1            67
[1] 2 2
[1] FALSE
D75V10, binary
               cls
clus              0   1
  RB1 MUTATED     1   8
  RB1 WILD-TYPE  35 231
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1    8
  RB1 WILD-TYPE   35  231
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            1            35
  YES           8           231
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, binary
               cls
clus              0   1
  RB1 MUTATED     4   5
  RB1 WILD-TYPE 102 165
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      4    5
  RB1 WILD-TYPE  102  165
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           4           102
  MALE             5           165
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       0                         0     9
  RB1 WILD-TYPE     3                         1   263
D75V13, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               9           263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
               cls
clus              0   1
  RB1 MUTATED     0   9
  RB1 WILD-TYPE   3 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    9
  RB1 WILD-TYPE    3  260
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           9           260
[1] 2 2
[1] FALSE

Clustering(76) Variable = CCK MUTATION ANALYSIS
D76V1, survival
               sevent
clus2             0   1
  CCK MUTATED     5   1
  CCK WILD-TYPE 121 139
  CCK MUTATED CCK WILD-TYPE 
            6           260 
  CCK MUTATED CCK WILD-TYPE 
            1           139 
$`CCK MUTATED`
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GJ TCGA-EE-A3JB TCGA-FS-A1ZT TCGA-GN-A265 
       62.79         8.84        19.43         0.95        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        36.85         1.08        39.62 
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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        47.21        30.08 
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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15         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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        31.33 
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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CCK MUTATED CCK WILD-TYPE 
         0.95          0.13 
  CCK MUTATED CCK WILD-TYPE 
        84.72        125.65 
  CCK MUTATED CCK WILD-TYPE 
       30.035        16.355 
[1] "0.9 - 84.7 (30.0)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "3.8"
D76V2, survival
               sevent
clus2             0   1
  CCK MUTATED     5   1
  CCK WILD-TYPE 124 140
  CCK MUTATED CCK WILD-TYPE 
            6           264 
  CCK MUTATED CCK WILD-TYPE 
            1           140 
$`CCK MUTATED`
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GJ TCGA-EE-A3JB TCGA-FS-A1ZT TCGA-GN-A265 
       63.78        14.47        89.33       201.80        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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        64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        2.04        11.74       139.89       117.93        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  CCK MUTATED CCK WILD-TYPE 
        14.47          0.16 
  CCK MUTATED CCK WILD-TYPE 
       201.80        357.37 
  CCK MUTATED CCK WILD-TYPE 
        74.25         51.12 
[1] "14.5 - 201.8 (74.2)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "3.7"
D76V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  CCK MUTATED                    1             0
  CCK WILD-TYPE                 38             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CCK MUTATED                                           1                   4
  CCK WILD-TYPE                                        59                 167
D76V4, multiclass
                                           clus
vv                                          CCK MUTATED CCK WILD-TYPE
  DISTANT METASTASIS                                  1            38
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           1            59
  REGIONAL LYMPH NODE                                 4           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
  CCK MUTATED             0       0       0        1        0        0
  CCK WILD-TYPE          10       6      24        9       24       16
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CCK MUTATED           0         0         0         2          0          1
  CCK WILD-TYPE        10        14         9        30         13         22
               vv
clus            STAGE IIIC STAGE IV
  CCK MUTATED            1        0
  CCK WILD-TYPE         45       16
D76V5, multiclass
             clus
vv            CCK MUTATED CCK WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            24
  STAGE IA              1             9
  STAGE IB              0            24
  STAGE II              0            16
  STAGE IIA             0            10
  STAGE IIB             0            14
  STAGE IIC             0             9
  STAGE III             2            30
  STAGE IIIA            0            13
  STAGE IIIB            1            22
  STAGE IIIC            1            45
  STAGE IV              0            16
[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  3  0
  CCK WILD-TYPE    51 58 51 57
D76V6, multiclass
       clus
vv      CCK MUTATED CCK WILD-TYPE
  T0+T1           1            51
  T2              1            58
  T3              3            51
  T4              0            57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CCK MUTATED     1   4   0   0
  CCK WILD-TYPE 138  44  33  36
D76V7, multiclass
    clus
vv   CCK MUTATED CCK WILD-TYPE
  N0           1           138
  N1           4            44
  N2           0            33
  N3           0            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             M0  M1 M1A M1B M1C
  CCK MUTATED     5   0   0   0   0
  CCK WILD-TYPE 239   4   3   2   8
D76V8, multiclass
     clus
vv    CCK MUTATED CCK WILD-TYPE
  M0            5           239
  M1            0             4
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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 101  67
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      2    1
  CCK WILD-TYPE  101   67
     clus
vv    CCK MUTATED CCK WILD-TYPE
  NO            2           101
  YES           1            67
[1] 2 2
[1] FALSE
D76V10, binary
               cls
clus              0   1
  CCK MUTATED     1   5
  CCK WILD-TYPE  35 234
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      1    5
  CCK WILD-TYPE   35  234
     clus
vv    CCK MUTATED CCK WILD-TYPE
  NO            1            35
  YES           5           234
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, binary
               cls
clus              0   1
  CCK MUTATED     2   4
  CCK WILD-TYPE 104 166
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      2    4
  CCK WILD-TYPE  104  166
        clus
vv       CCK MUTATED CCK WILD-TYPE
  FEMALE           2           104
  MALE             4           166
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCK MUTATED       0                         0     6
  CCK WILD-TYPE     3                         1   266
D76V13, multiclass
                           clus
vv                          CCK MUTATED CCK WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               6           266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
               cls
clus              0   1
  CCK MUTATED     0   6
  CCK WILD-TYPE   3 263
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      0    6
  CCK WILD-TYPE    3  263
                        clus
vv                       CCK MUTATED CCK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           6           263
[1] 2 2
[1] FALSE

Clustering(77) Variable = ZNF780B MUTATION ANALYSIS
D77V1, survival
                   sevent
clus2                 0   1
  ZNF780B MUTATED     7   3
  ZNF780B WILD-TYPE 119 137
  ZNF780B MUTATED ZNF780B WILD-TYPE 
               10               256 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                3               137 
$`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        60.49        30.15 
TCGA-EE-A3AG TCGA-ER-A2NF TCGA-FW-A3R5 TCGA-GF-A6C9 
       15.95        13.08         0.99        11.61 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       36.33        51.12        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        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       125.65       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        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31       122.73        51.62         3.68        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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  ZNF780B MUTATED ZNF780B WILD-TYPE 
             0.99              0.13 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
            60.49            125.65 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           16.965            16.900 
[1] "1.0 - 60.5 (17.0)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.8"
D77V2, survival
                   sevent
clus2                 0   1
  ZNF780B MUTATED     7   3
  ZNF780B WILD-TYPE 122 138
  ZNF780B MUTATED ZNF780B WILD-TYPE 
               10               260 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                3               138 
$`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       134.40        54.51 
TCGA-EE-A3AG TCGA-ER-A2NF TCGA-FW-A3R5 TCGA-GF-A6C9 
       23.47        16.37        22.92        11.74 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       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       158.63       203.05       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       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62         3.68        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      148.18        79.99        43.82        23.34        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ZNF780B MUTATED ZNF780B WILD-TYPE 
            11.74              0.16 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           314.56            357.37 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           47.560            52.585 
[1] "11.7 - 314.6 (47.6)" "0.2 - 357.4 (52.6)" 
[1] "hr=" "2.1"
D77V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  ZNF780B MUTATED                    1             1
  ZNF780B WILD-TYPE                 38             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ZNF780B MUTATED                                           2
  ZNF780B WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  ZNF780B MUTATED                     6
  ZNF780B WILD-TYPE                 165
D77V4, multiclass
                                           clus
vv                                          ZNF780B MUTATED ZNF780B WILD-TYPE
  DISTANT METASTASIS                                      1                38
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                58
  REGIONAL LYMPH NODE                                     6               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
  ZNF780B MUTATED             0       0       1        1        1        1
  ZNF780B WILD-TYPE          10       6      23        9       23       15
                   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        30         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  ZNF780B MUTATED            1          1        0
  ZNF780B WILD-TYPE         22         45       16
D77V5, multiclass
             clus
vv            ZNF780B MUTATED ZNF780B WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   1                23
  STAGE IA                  1                 9
  STAGE IB                  1                23
  STAGE II                  1                15
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 0                 9
  STAGE III                 2                30
  STAGE IIIA                0                13
  STAGE IIIB                1                22
  STAGE IIIC                1                45
  STAGE IV                  0                16
[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    50 57 52 55
D77V6, multiclass
       clus
vv      ZNF780B MUTATED ZNF780B WILD-TYPE
  T0+T1               2                50
  T2                  2                57
  T3                  2                52
  T4                  2                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
  ZNF780B MUTATED     6   0   2   1
  ZNF780B WILD-TYPE 133  48  31  35
D77V7, multiclass
    clus
vv   ZNF780B MUTATED ZNF780B WILD-TYPE
  N0               6               133
  N1               0                48
  N2               2                31
  N3               1                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  ZNF780B MUTATED     9   0   0   0   0
  ZNF780B WILD-TYPE 235   4   3   2   8
D77V8, multiclass
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  M0                9               235
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 100  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      3    4
  ZNF780B WILD-TYPE  100   64
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  NO                3               100
  YES               4                64
[1] 2 2
[1] FALSE
D77V10, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     2   8
  ZNF780B WILD-TYPE  34 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      2    8
  ZNF780B WILD-TYPE   34  231
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  NO                2                34
  YES               8               231
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     2   8
  ZNF780B WILD-TYPE 104 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      2    8
  ZNF780B WILD-TYPE  104  162
        clus
vv       ZNF780B MUTATED ZNF780B WILD-TYPE
  FEMALE               2               104
  MALE                 8               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF780B MUTATED       0                         0    10
  ZNF780B WILD-TYPE     3                         1   262
D77V13, multiclass
                           clus
vv                          ZNF780B MUTATED ZNF780B WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10               262
[1] 3 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  10
  ZNF780B WILD-TYPE   3 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      0   10
  ZNF780B WILD-TYPE    3  259
                        clus
vv                       ZNF780B MUTATED ZNF780B WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               259
[1] 2 2
[1] FALSE

Clustering(78) Variable = ATP5F1 MUTATION ANALYSIS
D78V1, survival
                  sevent
clus2                0   1
  ATP5F1 MUTATED     4   3
  ATP5F1 WILD-TYPE 122 137
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              259 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               3              137 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        62.79         8.55        36.85        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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        55.69 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
            0.99             0.13 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           34.98           125.65 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
            8.84            17.33 
[1] "1.0 - 35.0 (8.8)"   "0.1 - 125.7 (17.3)"
[1] "hr=" "1.2"
D78V2, survival
                  sevent
clus2                0   1
  ATP5F1 MUTATED     4   3
  ATP5F1 WILD-TYPE 125 138
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               7              263 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               3              138 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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 
       63.78        72.07        64.64        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
            2.60             0.16 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           54.51           357.37 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           22.92            53.19 
[1] "2.6 - 54.5 (22.9)"  "0.2 - 357.4 (53.2)"
[1] "hr=" "1.9"
D78V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ATP5F1 MUTATED                    0             0
  ATP5F1 WILD-TYPE                 39             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ATP5F1 MUTATED                                           1
  ATP5F1 WILD-TYPE                                        59
                  vv
clus               REGIONAL LYMPH NODE
  ATP5F1 MUTATED                     6
  ATP5F1 WILD-TYPE                 165
D78V4, multiclass
                                           clus
vv                                          ATP5F1 MUTATED ATP5F1 WILD-TYPE
  DISTANT METASTASIS                                     0               39
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               59
  REGIONAL LYMPH NODE                                    6              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
  ATP5F1 MUTATED             0       0       1        2        0        0
  ATP5F1 WILD-TYPE          10       6      23        8       24       16
                  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        31         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ATP5F1 MUTATED            1          1        0
  ATP5F1 WILD-TYPE         22         45       16
D78V5, multiclass
             clus
vv            ATP5F1 MUTATED ATP5F1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 2                8
  STAGE IB                 0               24
  STAGE II                 0               16
  STAGE IIA                1                9
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               31
  STAGE IIIA               0               13
  STAGE IIIB               1               22
  STAGE IIIC               1               45
  STAGE IV                 0               16
[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    50 58 53 55
D78V6, multiclass
       clus
vv      ATP5F1 MUTATED ATP5F1 WILD-TYPE
  T0+T1              2               50
  T2                 1               58
  T3                 1               53
  T4                 2               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
  ATP5F1 MUTATED     4   1   1   1
  ATP5F1 WILD-TYPE 135  47  32  35
D78V7, multiclass
    clus
vv   ATP5F1 MUTATED ATP5F1 WILD-TYPE
  N0              4              135
  N1              1               47
  N2              1               32
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ATP5F1 MUTATED     7   0   0   0   0
  ATP5F1 WILD-TYPE 237   4   3   2   8
D78V8, multiclass
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  M0               7              237
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 99 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      4    2
  ATP5F1 WILD-TYPE   99   66
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  NO               4               99
  YES              2               66
[1] 2 2
[1] FALSE
D78V10, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     0   7
  ATP5F1 WILD-TYPE  36 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      0    7
  ATP5F1 WILD-TYPE   36  232
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  NO               0               36
  YES              7              232
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     1   6
  ATP5F1 WILD-TYPE 105 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      1    6
  ATP5F1 WILD-TYPE  105  164
        clus
vv       ATP5F1 MUTATED ATP5F1 WILD-TYPE
  FEMALE              1              105
  MALE                6              164
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP5F1 MUTATED       0                         0     7
  ATP5F1 WILD-TYPE     3                         1   265
D78V13, multiclass
                           clus
vv                          ATP5F1 MUTATED ATP5F1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  7              265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     0   7
  ATP5F1 WILD-TYPE   3 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      0    7
  ATP5F1 WILD-TYPE    3  262
                        clus
vv                       ATP5F1 MUTATED ATP5F1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7              262
[1] 2 2
[1] FALSE

Clustering(79) Variable = LOC728819 MUTATION ANALYSIS
D79V1, survival
                     sevent
clus2                   0   1
  LOC728819 MUTATED     5   3
  LOC728819 WILD-TYPE 121 137
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  8                 258 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  3                 137 
$`LOC728819 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-DA-A1I7 TCGA-EE-A3AA TCGA-ER-A19P 
       16.47        10.29        86.76        36.69       124.31        34.68 
TCGA-FW-A3R5 TCGA-RP-A693 
        0.99         0.33 

$`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        44.19         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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
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-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       16.24        15.42        12.16        14.70         5.79         0.69 

  LOC728819 MUTATED LOC728819 WILD-TYPE 
               0.33                0.13 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
             124.31              125.65 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
             25.575              16.785 
[1] "0.3 - 124.3 (25.6)" "0.1 - 125.7 (16.8)"
[1] "hr=" "1.7"
D79V2, survival
                     sevent
clus2                   0   1
  LOC728819 MUTATED     5   3
  LOC728819 WILD-TYPE 124 138
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  8                 262 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  3                 138 
$`LOC728819 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-DA-A1I7 TCGA-EE-A3AA TCGA-ER-A19P 
       16.57        43.43        86.76        61.18       124.31       162.08 
TCGA-FW-A3R5 TCGA-RP-A693 
       22.92         0.33 

$`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        62.07       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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       32.48        39.58         6.67         0.69 

  LOC728819 MUTATED LOC728819 WILD-TYPE 
               0.33                0.16 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
             162.08              357.37 
  LOC728819 MUTATED LOC728819 WILD-TYPE 
             52.305              51.815 
[1] "0.3 - 162.1 (52.3)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.2"
D79V3, continuous
                     vv
clus                  DISTANT METASTASIS PRIMARY TUMOR
  LOC728819 MUTATED                    1             0
  LOC728819 WILD-TYPE                 38             5
                     vv
clus                  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  LOC728819 MUTATED                                           1
  LOC728819 WILD-TYPE                                        59
                     vv
clus                  REGIONAL LYMPH NODE
  LOC728819 MUTATED                     6
  LOC728819 WILD-TYPE                 165
D79V4, multiclass
                                           clus
vv                                          LOC728819 MUTATED
  DISTANT METASTASIS                                        1
  PRIMARY TUMOR                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                 1
  REGIONAL LYMPH NODE                                       6
                                           clus
vv                                          LOC728819 WILD-TYPE
  DISTANT METASTASIS                                         38
  PRIMARY TUMOR                                               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                  59
  REGIONAL LYMPH NODE                                       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
  LOC728819 MUTATED             0       0       0        0        0        0
  LOC728819 WILD-TYPE          10       6      24       10       24       16
                     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        29         13
                     vv
clus                  STAGE IIIB STAGE IIIC STAGE IV
  LOC728819 MUTATED            1          1        1
  LOC728819 WILD-TYPE         22         45       15
D79V5, multiclass
             clus
vv            LOC728819 MUTATED LOC728819 WILD-TYPE
  I OR II NOS                 0                  10
  STAGE 0                     0                   6
  STAGE I                     0                  24
  STAGE IA                    0                  10
  STAGE IB                    0                  24
  STAGE II                    0                  16
  STAGE IIA                   0                  10
  STAGE IIB                   1                  13
  STAGE IIC                   0                   9
  STAGE III                   3                  29
  STAGE IIIA                  0                  13
  STAGE IIIB                  1                  22
  STAGE IIIC                  1                  45
  STAGE IV                    1                  15
[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    48 59 53 57
D79V6, multiclass
       clus
vv      LOC728819 MUTATED LOC728819 WILD-TYPE
  T0+T1                 4                  48
  T2                    0                  59
  T3                    1                  53
  T4                    0                  57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  LOC728819 MUTATED     2   0   4   1
  LOC728819 WILD-TYPE 137  48  29  35
D79V7, multiclass
    clus
vv   LOC728819 MUTATED LOC728819 WILD-TYPE
  N0                 2                 137
  N1                 0                  48
  N2                 4                  29
  N3                 1                  35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   M0  M1 M1A M1B M1C
  LOC728819 MUTATED     7   0   0   0   1
  LOC728819 WILD-TYPE 237   4   3   2   7
D79V8, multiclass
     clus
vv    LOC728819 MUTATED LOC728819 WILD-TYPE
  M0                  7                 237
  M1                  0                   4
  M1A                 0                   3
  M1B                 0                   2
  M1C                 1                   7
[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 102  67
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      1    1
  LOC728819 WILD-TYPE  102   67
     clus
vv    LOC728819 MUTATED LOC728819 WILD-TYPE
  NO                  1                 102
  YES                 1                  67
[1] 2 2
[1] FALSE
D79V10, binary
                     cls
clus                    0   1
  LOC728819 MUTATED     4   4
  LOC728819 WILD-TYPE  32 235
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      4    4
  LOC728819 WILD-TYPE   32  235
     clus
vv    LOC728819 MUTATED LOC728819 WILD-TYPE
  NO                  4                  32
  YES                 4                 235
[1] 2 2
[1] FALSE
D79V11, continuous
[1] "Remove cluster labels:" "LOC728819 MUTATED"     
clus
  LOC728819 MUTATED LOC728819 WILD-TYPE 
                  2                 202 
         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-A2MF          TCGA-EE-A2MG          TCGA-EE-A2MH 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MI          TCGA-EE-A2MJ          TCGA-EE-A2MK 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2ML          TCGA-EE-A2MM          TCGA-EE-A2MN 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MP          TCGA-EE-A2MQ          TCGA-EE-A2MR 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A2MS          TCGA-EE-A2MT          TCGA-EE-A2MU 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3AE          TCGA-EE-A3AH          TCGA-EE-A3J3 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3J4          TCGA-EE-A3J5          TCGA-EE-A3J7 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3J8          TCGA-EE-A3JA          TCGA-EE-A3JB 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-EE-A3JE          TCGA-EE-A3JH          TCGA-EE-A3JI 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A197          TCGA-ER-A198          TCGA-ER-A199 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A19C          TCGA-ER-A19D          TCGA-ER-A19E 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A19F          TCGA-ER-A19G          TCGA-ER-A19H 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-ER-A19M          TCGA-ER-A19Q          TCGA-ER-A19T 
"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-ER-A42K          TCGA-FR-A3YN          TCGA-FR-A44A 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1YW          TCGA-FS-A1YX          TCGA-FS-A1YY 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1Z0          TCGA-FS-A1Z4          TCGA-FS-A1Z7 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZA          TCGA-FS-A1ZB          TCGA-FS-A1ZD 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZE          TCGA-FS-A1ZF          TCGA-FS-A1ZG 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZH          TCGA-FS-A1ZJ          TCGA-FS-A1ZK 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZM          TCGA-FS-A1ZP          TCGA-FS-A1ZR 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZS          TCGA-FS-A1ZT          TCGA-FS-A1ZU 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A1ZW          TCGA-FS-A1ZY          TCGA-FS-A1ZZ 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A4F0          TCGA-FS-A4F4          TCGA-FS-A4F5 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A4F8          TCGA-FS-A4F9          TCGA-FS-A4FB 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-FS-A4FC          TCGA-FS-A4FD          TCGA-FW-A3TV 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-GF-A6C8          TCGA-GN-A262          TCGA-GN-A264 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-GN-A267          TCGA-GN-A268          TCGA-GN-A26A 
"LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" "LOC728819 WILD-TYPE" 
         TCGA-GN-A26D 
"LOC728819 WILD-TYPE" 
D79V12, binary
                     cls
clus                    0   1
  LOC728819 MUTATED     3   5
  LOC728819 WILD-TYPE 103 165
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      3    5
  LOC728819 WILD-TYPE  103  165
        clus
vv       LOC728819 MUTATED LOC728819 WILD-TYPE
  FEMALE                 3                 103
  MALE                   5                 165
[1] 2 2
[1] FALSE
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LOC728819 MUTATED       0                         0     8
  LOC728819 WILD-TYPE     3                         1   264
D79V13, multiclass
                           clus
vv                          LOC728819 MUTATED LOC728819 WILD-TYPE
  ASIAN                                     0                   3
  BLACK OR AFRICAN AMERICAN                 0                   1
  WHITE                                     8                 264
[1] 3 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   8
  LOC728819 WILD-TYPE   3 261
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC728819 MUTATED      0    8
  LOC728819 WILD-TYPE    3  261
                        clus
vv                       LOC728819 MUTATED LOC728819 WILD-TYPE
  HISPANIC OR LATINO                     0                   3
  NOT HISPANIC OR LATINO                 8                 261
[1] 2 2
[1] FALSE

Clustering(80) Variable = LACRT MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  LACRT MUTATED     5   3
  LACRT WILD-TYPE 121 137
  LACRT MUTATED LACRT WILD-TYPE 
              8             258 
  LACRT MUTATED LACRT WILD-TYPE 
              3             137 
$`LACRT MUTATED`
TCGA-D3-A2JN TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-EE-A29M TCGA-EE-A2GR 
       56.19        32.61        25.78        47.87        39.62         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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       44.19         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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.28        21.44        52.01        13.68        17.72        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        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        55.69         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-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.85        11.61        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  LACRT MUTATED LACRT WILD-TYPE 
           0.99            0.13 
  LACRT MUTATED LACRT WILD-TYPE 
          56.19          125.65 
  LACRT MUTATED LACRT WILD-TYPE 
         29.195          16.355 
[1] "1.0 - 56.2 (29.2)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1.5"
D80V2, survival
                 sevent
clus2               0   1
  LACRT MUTATED     5   3
  LACRT WILD-TYPE 124 138
  LACRT MUTATED LACRT WILD-TYPE 
              8             262 
  LACRT MUTATED LACRT WILD-TYPE 
              3             138 
$`LACRT MUTATED`
TCGA-D3-A2JN TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-EE-A29M TCGA-EE-A2GR 
       56.19        63.81        26.89       137.92        56.84        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       62.07       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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.94        22.62       135.75       178.32        18.18       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        22.29 
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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  LACRT MUTATED LACRT WILD-TYPE 
          10.13            0.16 
  LACRT MUTATED LACRT WILD-TYPE 
         137.92          357.37 
  LACRT MUTATED LACRT WILD-TYPE 
         41.540          51.815 
[1] "10.1 - 137.9 (41.5)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1.1"
D80V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  LACRT MUTATED                    2             0
  LACRT WILD-TYPE                 37             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  LACRT MUTATED                                           2                   5
  LACRT WILD-TYPE                                        58                 166
D80V4, multiclass
                                           clus
vv                                          LACRT MUTATED LACRT WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   5             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
  LACRT MUTATED             1       0       0        0        1        2
  LACRT WILD-TYPE           9       6      24       10       23       14
                 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        30         13         23
                 vv
clus              STAGE IIIC STAGE IV
  LACRT MUTATED            1        0
  LACRT WILD-TYPE         45       16
D80V5, multiclass
             clus
vv            LACRT MUTATED LACRT WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              14
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    51 57 53 54
D80V6, multiclass
       clus
vv      LACRT MUTATED LACRT WILD-TYPE
  T0+T1             1              51
  T2                2              57
  T3                1              53
  T4                3              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
  LACRT MUTATED     5   2   1   0
  LACRT WILD-TYPE 134  46  32  36
D80V7, multiclass
    clus
vv   LACRT MUTATED LACRT WILD-TYPE
  N0             5             134
  N1             2              46
  N2             1              32
  N3             0              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               M0  M1 M1A M1B M1C
  LACRT MUTATED     8   0   0   0   0
  LACRT WILD-TYPE 236   4   3   2   8
D80V8, multiclass
     clus
vv    LACRT MUTATED LACRT WILD-TYPE
  M0              8             236
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 101  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      2    1
  LACRT WILD-TYPE  101   67
     clus
vv    LACRT MUTATED LACRT WILD-TYPE
  NO              2             101
  YES             1              67
[1] 2 2
[1] FALSE
D80V10, binary
                 cls
clus                0   1
  LACRT MUTATED     2   7
  LACRT WILD-TYPE  34 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      2    7
  LACRT WILD-TYPE   34  232
     clus
vv    LACRT MUTATED LACRT WILD-TYPE
  NO              2              34
  YES             7             232
[1] 2 2
[1] FALSE
D80V11, continuous
D80V12, binary
                 cls
clus                0   1
  LACRT MUTATED     4   5
  LACRT WILD-TYPE 102 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      4    5
  LACRT WILD-TYPE  102  165
        clus
vv       LACRT MUTATED LACRT WILD-TYPE
  FEMALE             4             102
  MALE               5             165
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LACRT MUTATED       0                         0     9
  LACRT WILD-TYPE     3                         1   263
D80V13, multiclass
                           clus
vv                          LACRT MUTATED LACRT WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                 cls
clus                0   1
  LACRT MUTATED     0   9
  LACRT WILD-TYPE   3 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACRT MUTATED      0    9
  LACRT WILD-TYPE    3  260
                        clus
vv                       LACRT MUTATED LACRT WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             260
[1] 2 2
[1] FALSE

Clustering(81) Variable = RPGRIP1 MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  RPGRIP1 MUTATED    13  10
  RPGRIP1 WILD-TYPE 113 130
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               23               243 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               10               130 
$`RPGRIP1 MUTATED`
TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A29D 
       25.78        13.22         6.64        14.83        13.22        11.15 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2M5 TCGA-EE-A2MF TCGA-EE-A2MI 
       62.79         8.84        34.29         8.84         2.73        14.56 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JI 
       60.49        53.16        52.67        21.60        27.35        33.60 
TCGA-FS-A1ZP TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A267 
       52.08        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       54.31        32.28        21.44        32.61        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        19.00        13.35        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 
       60.23         4.34        15.85         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        36.85         1.08        39.62 
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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       51.12        17.98        60.00        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        55.69         5.42 
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-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       125.65       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       21.60         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82         5.23         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       10.78         5.98         6.41         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        10.13        15.42        12.16        14.70 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             0.99              0.13 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
            62.79            125.65 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
            16.24             17.33 
[1] "1.0 - 62.8 (16.2)"  "0.1 - 125.7 (17.3)"
[1] "hr=" "1.2"
D81V2, survival
                   sevent
clus2                 0   1
  RPGRIP1 MUTATED    14  10
  RPGRIP1 WILD-TYPE 115 131
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               24               246 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
               10               131 
$`RPGRIP1 MUTATED`
TCGA-D3-A51T TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EB-A5UN 
       26.89         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-A2MF 
       13.97        63.78        14.47        67.43        21.67       268.73 
TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JD 
      204.66       134.40       162.48        71.21        36.95        27.35 
TCGA-EE-A3JI TCGA-FS-A1ZP TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-GN-A267 
      148.08        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        32.94        22.62        63.81       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29 
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       133.81       151.27        91.56 
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 
       64.64         2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        59.28       314.56       161.03 
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       126.81        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       158.63       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        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       109.58        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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93       101.26       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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             3.65              0.16 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
           268.73            357.37 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
           65.345            50.825 
[1] "3.6 - 268.7 (65.3)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1.4"
D81V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  RPGRIP1 MUTATED                    2             1
  RPGRIP1 WILD-TYPE                 37             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  RPGRIP1 MUTATED                                           3
  RPGRIP1 WILD-TYPE                                        57
                   vv
clus                REGIONAL LYMPH NODE
  RPGRIP1 MUTATED                    19
  RPGRIP1 WILD-TYPE                 152
D81V4, multiclass
                                           clus
vv                                          RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  DISTANT METASTASIS                                      2                37
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                57
  REGIONAL LYMPH NODE                                    19               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       4        0        1        2
  RPGRIP1 WILD-TYPE          10       6      20       10       23       14
                   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        29         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  RPGRIP1 MUTATED            3          4        1
  RPGRIP1 WILD-TYPE         20         42       15
D81V5, multiclass
             clus
vv            RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   4                20
  STAGE IA                  0                10
  STAGE IB                  1                23
  STAGE II                  2                14
  STAGE IIA                 0                10
  STAGE IIB                 3                11
  STAGE IIC                 1                 8
  STAGE III                 3                29
  STAGE IIIA                2                11
  STAGE IIIB                3                20
  STAGE IIIC                4                42
  STAGE IV                  1                15
[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  7  8  6
  RPGRIP1 WILD-TYPE    51 52 46 51
D81V6, multiclass
       clus
vv      RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  T0+T1               1                51
  T2                  7                52
  T3                  8                46
  T4                  6                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
  RPGRIP1 MUTATED    10   7   5   1
  RPGRIP1 WILD-TYPE 129  41  28  35
D81V7, multiclass
    clus
vv   RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  N0              10               129
  N1               7                41
  N2               5                28
  N3               1                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  RPGRIP1 MUTATED    24   0   0   0   1
  RPGRIP1 WILD-TYPE 220   4   3   2   7
D81V8, multiclass
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  M0               24               220
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               1                 7
[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 90 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED     13    5
  RPGRIP1 WILD-TYPE   90   63
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  NO               13                90
  YES               5                63
[1] 2 2
[1] FALSE
D81V10, binary
                   cls
clus                  0   1
  RPGRIP1 MUTATED     1  24
  RPGRIP1 WILD-TYPE  35 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      1   24
  RPGRIP1 WILD-TYPE   35  215
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  NO                1                35
  YES              24               215
[1] 2 2
[1] FALSE
D81V11, continuous
D81V12, binary
                   cls
clus                  0   1
  RPGRIP1 MUTATED     5  20
  RPGRIP1 WILD-TYPE 101 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      5   20
  RPGRIP1 WILD-TYPE  101  150
        clus
vv       RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  FEMALE               5               101
  MALE                20               150
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPGRIP1 MUTATED       0                         0    25
  RPGRIP1 WILD-TYPE     3                         1   247
D81V13, multiclass
                           clus
vv                          RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  25               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"
D81V14, binary
                   cls
clus                  0   1
  RPGRIP1 MUTATED     0  25
  RPGRIP1 WILD-TYPE   3 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      0   25
  RPGRIP1 WILD-TYPE    3  244
                        clus
vv                       RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              25               244
[1] 2 2
[1] FALSE

Clustering(82) Variable = THEMIS MUTATION ANALYSIS
D82V1, survival
                  sevent
clus2                0   1
  THEMIS MUTATED    19  13
  THEMIS WILD-TYPE 107 127
  THEMIS MUTATED THEMIS WILD-TYPE 
              32              234 
  THEMIS MUTATED THEMIS WILD-TYPE 
              13              127 
$`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        36.85 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MS 
        1.08         8.09        34.29        55.69         8.84        53.16 
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-GF-A6C9 TCGA-QB-A6FS 
       11.61         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        86.76        11.41        44.19 
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        59.57       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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       25.78        52.01        13.68        17.72        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY 
       21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       13.22        10.55         6.31         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        60.23         4.34        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
        1.18         7.99         9.90        62.79         8.55        39.62 
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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       51.12        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        60.49        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
      122.73        51.62         3.68        13.81        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       22.92        16.14         0.95        27.35        18.41        21.73 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
       33.60        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-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-A4FB 
        5.23        53.85         7.36        28.73        14.20         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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         0.85        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       16.24        15.42        12.16        14.70         0.33         0.69 

  THEMIS MUTATED THEMIS WILD-TYPE 
            0.99             0.13 
  THEMIS MUTATED THEMIS WILD-TYPE 
           92.42           125.65 
  THEMIS MUTATED THEMIS WILD-TYPE 
          21.600           16.355 
[1] "1.0 - 92.4 (21.6)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1.3"
D82V2, survival
                  sevent
clus2                0   1
  THEMIS MUTATED    19  13
  THEMIS WILD-TYPE 110 128
  THEMIS MUTATED THEMIS WILD-TYPE 
              32              238 
  THEMIS MUTATED THEMIS WILD-TYPE 
              13              128 
$`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        64.64 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MS 
        2.60        37.35        67.43       126.81        21.67       162.48 
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-GF-A6C9 TCGA-QB-A6FS 
       11.74         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        86.76        11.87        62.07 
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        59.57       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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       26.89       135.75       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        36.82        39.29        86.14        59.28       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      134.40        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
        3.68        13.81        23.47       172.18       127.20        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      201.80        27.35        51.35       109.58       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-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-A19T TCGA-ER-A19W 
       61.05        44.05       162.08        50.89         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       66.67        28.73       174.84        26.73        49.45         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16        19.30         9.90         7.23         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         0.33         0.69 

  THEMIS MUTATED THEMIS WILD-TYPE 
            2.60             0.16 
  THEMIS MUTATED THEMIS WILD-TYPE 
          171.58           357.37 
  THEMIS MUTATED THEMIS WILD-TYPE 
          48.365           52.585 
[1] "2.6 - 171.6 (48.4)" "0.2 - 357.4 (52.6)"
[1] "hr=" "1.1"
D82V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  THEMIS MUTATED                    4             0
  THEMIS WILD-TYPE                 35             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  THEMIS MUTATED                                           7
  THEMIS WILD-TYPE                                        53
                  vv
clus               REGIONAL LYMPH NODE
  THEMIS MUTATED                    22
  THEMIS WILD-TYPE                 149
D82V4, multiclass
                                           clus
vv                                          THEMIS MUTATED THEMIS WILD-TYPE
  DISTANT METASTASIS                                     4               35
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              7               53
  REGIONAL LYMPH NODE                                   22              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
  THEMIS MUTATED             1       1       2        3        3        4
  THEMIS WILD-TYPE           9       5      22        7       21       12
                  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        29         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  THEMIS MUTATED            4          6        1
  THEMIS WILD-TYPE         19         40       15
D82V5, multiclass
             clus
vv            THEMIS MUTATED THEMIS WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  1                5
  STAGE I                  2               22
  STAGE IA                 3                7
  STAGE IB                 3               21
  STAGE II                 4               12
  STAGE IIA                0               10
  STAGE IIB                3               11
  STAGE IIC                0                9
  STAGE III                3               29
  STAGE IIIA               1               12
  STAGE IIIB               4               19
  STAGE IIIC               6               40
  STAGE IV                 1               15
[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    46 53 46 51
D82V6, multiclass
       clus
vv      THEMIS MUTATED THEMIS WILD-TYPE
  T0+T1              6               46
  T2                 6               53
  T3                 8               46
  T4                 6               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
  THEMIS MUTATED    19   2   5   5
  THEMIS WILD-TYPE 120  46  28  31
D82V7, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  N0             19              120
  N1              2               46
  N2              5               28
  N3              5               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
  THEMIS MUTATED    30   1   0   0   0
  THEMIS WILD-TYPE 214   3   3   2   8
D82V8, multiclass
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  M0              30              214
  M1               1                3
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 89 60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     14    8
  THEMIS WILD-TYPE   89   60
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO              14               89
  YES              8               60
[1] 2 2
[1] FALSE
D82V10, binary
                  cls
clus                 0   1
  THEMIS MUTATED     6  27
  THEMIS WILD-TYPE  30 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      6   27
  THEMIS WILD-TYPE   30  212
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO               6               30
  YES             27              212
[1] 2 2
[1] FALSE
D82V11, continuous
D82V12, binary
                  cls
clus                 0   1
  THEMIS MUTATED     9  24
  THEMIS WILD-TYPE  97 146
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      9   24
  THEMIS WILD-TYPE   97  146
        clus
vv       THEMIS MUTATED THEMIS WILD-TYPE
  FEMALE              9               97
  MALE               24              146
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THEMIS MUTATED       0                         0    33
  THEMIS WILD-TYPE     3                         1   239
D82V13, multiclass
                           clus
vv                          THEMIS MUTATED THEMIS WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 33              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"
D82V14, binary
                  cls
clus                 0   1
  THEMIS MUTATED     0  32
  THEMIS WILD-TYPE   3 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      0   32
  THEMIS WILD-TYPE    3  237
                        clus
vv                       THEMIS MUTATED THEMIS WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             32              237
[1] 2 2
[1] FALSE

Clustering(83) Variable = PTPRT MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2               0   1
  PTPRT MUTATED    44  33
  PTPRT WILD-TYPE  82 107
  PTPRT MUTATED PTPRT WILD-TYPE 
             77             189 
  PTPRT MUTATED PTPRT WILD-TYPE 
             33             107 
$`PTPRT MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       70.16        45.83        44.19        36.16        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E 
       59.57        15.25        46.98         6.31       103.59        93.21 
TCGA-D3-A51T TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 
       25.78        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        62.79        36.85        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        51.12        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-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM 
       98.27         9.53         2.73        14.56        63.42        56.02 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       21.60        60.49        53.16         5.56       124.31        51.62 
TCGA-EE-A3AH TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19G TCGA-ER-A2NE TCGA-ER-A2NH 
       12.72        22.22        27.35       114.15         1.51        11.74 
TCGA-ER-A3PL TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ 
        1.71         7.33         7.30         8.22        12.89         8.65 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GF-A6C8 
       49.15         5.23        53.85         6.41         0.99         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-RP-A693 TCGA-RP-A694 
       44.28        31.33        10.13         0.33         0.69 

$`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        86.76        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        29.23        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       54.31        32.28        21.44        32.61        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-EB-A5UL TCGA-EE-A17X 
       13.15         0.20        23.15        19.00        13.35        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       10.55         6.31         1.35         4.31        60.23        15.85 
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-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W 
        1.08        39.62         9.50         8.09         9.99        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD 
        8.09        11.31        36.30         9.67        36.33        17.98 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       60.00        19.43        16.01        35.54        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
        5.42        36.33         2.70         6.18        47.51        29.46 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       44.25         7.96       125.65       111.91        25.08        26.99 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       52.67       122.73         3.68        30.15        13.81        15.95 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        3.22        22.92        21.60        21.60        16.14         0.95 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90        11.11        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       78.44        11.80         1.87        13.08        12.62         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         5.62        18.41        85.74        15.72 
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-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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.92        47.38        52.08         8.81        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.39         0.82         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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        9.90         7.23        11.61        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

  PTPRT MUTATED PTPRT WILD-TYPE 
           0.33            0.13 
  PTPRT MUTATED PTPRT WILD-TYPE 
         124.31          125.65 
  PTPRT MUTATED PTPRT WILD-TYPE 
          15.25           17.33 
[1] "0.3 - 124.3 (15.2)" "0.1 - 125.7 (17.3)"
[1] "hr=" "1.4"
D83V2, survival
                 sevent
clus2               0   1
  PTPRT MUTATED    44  33
  PTPRT WILD-TYPE  85 108
  PTPRT MUTATED PTPRT WILD-TYPE 
             77             193 
  PTPRT MUTATED PTPRT WILD-TYPE 
             33             108 
$`PTPRT MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       71.80        90.90        62.07        42.08        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E 
       59.57        58.06        46.98        13.87       103.59       174.84 
TCGA-D3-A51T TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 
       26.89        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        63.78        64.64        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        59.28        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-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM 
      129.27        47.28       268.73       204.66        96.23       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       43.23       134.40       162.48        53.26       124.31        51.62 
TCGA-EE-A3AH TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19G TCGA-ER-A2NE TCGA-ER-A2NH 
      138.81        53.19        27.35       268.93        20.15        32.05 
TCGA-ER-A3PL TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       33.21         7.79        27.72        53.52        23.93       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GF-A6C8 
      148.80        27.02        77.82        49.45        22.92         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-RP-A693 TCGA-RP-A694 
      139.89       117.93        10.13         0.33         0.69 

$`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        86.76        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        45.30        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
      145.12        32.94        22.62        63.81       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81        91.56       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        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       18.61        37.35        55.92       195.02        17.92        46.82 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       36.82        39.29        86.14       314.56       161.03        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       126.81        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 
      158.63       203.05        47.54       248.65        71.21       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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32       201.80        51.35       109.58 
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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       23.34        16.37        31.27       247.04        80.32        46.98 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59       202.65        20.91        28.08        48.85       357.37 
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-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       74.73        11.41        53.16        26.56        49.48        27.09 
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        19.30         9.90         7.23 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       11.74        84.72        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        6.67 

  PTPRT MUTATED PTPRT WILD-TYPE 
           0.33            0.16 
  PTPRT MUTATED PTPRT WILD-TYPE 
         268.93          357.37 
  PTPRT MUTATED PTPRT WILD-TYPE 
          55.59           48.89 
[1] "0.3 - 268.9 (55.6)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.4"
D83V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PTPRT MUTATED                   15             2
  PTPRT WILD-TYPE                 24             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  PTPRT MUTATED                                          15                  48
  PTPRT WILD-TYPE                                        45                 123
D83V4, multiclass
                                           clus
vv                                          PTPRT MUTATED PTPRT WILD-TYPE
  DISTANT METASTASIS                                   15              24
  PRIMARY TUMOR                                         2               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            15              45
  REGIONAL LYMPH NODE                                  48             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
  PTPRT MUTATED             4       3       7        4        7        6
  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        22         10         17
                 vv
clus              STAGE IIIC STAGE IV
  PTPRT MUTATED           10        5
  PTPRT WILD-TYPE         36       11
D83V5, multiclass
             clus
vv            PTPRT MUTATED PTPRT WILD-TYPE
  I OR II NOS             4               6
  STAGE 0                 3               3
  STAGE I                 7              17
  STAGE IA                4               6
  STAGE IB                7              17
  STAGE II                6              10
  STAGE IIA               3               7
  STAGE IIB               5               9
  STAGE IIC               3               6
  STAGE III              10              22
  STAGE IIIA              3              10
  STAGE IIIB              6              17
  STAGE IIIC             10              36
  STAGE IV                5              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
  PTPRT MUTATED      16 16 17 15
  PTPRT WILD-TYPE    36 43 37 42
D83V6, multiclass
       clus
vv      PTPRT MUTATED PTPRT WILD-TYPE
  T0+T1            16              36
  T2               16              43
  T3               17              37
  T4               15              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PTPRT MUTATED   45 12 10  5
  PTPRT WILD-TYPE 94 36 23 31
D83V7, multiclass
    clus
vv   PTPRT MUTATED PTPRT WILD-TYPE
  N0            45              94
  N1            12              36
  N2            10              23
  N3             5              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
  PTPRT MUTATED    72   0   1   0   4
  PTPRT WILD-TYPE 172   4   2   2   4
D83V8, multiclass
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  M0             72             172
  M1              0               4
  M1A             1               2
  M1B             0               2
  M1C             4               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 72 51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     31   17
  PTPRT WILD-TYPE   72   51
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             31              72
  YES            17              51
[1] 2 2
[1] FALSE
D83V10, binary
                 cls
clus                0   1
  PTPRT MUTATED    13  67
  PTPRT WILD-TYPE  23 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     13   67
  PTPRT WILD-TYPE   23  172
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             13              23
  YES            67             172
[1] 2 2
[1] FALSE
D83V11, continuous
D83V12, binary
                 cls
clus                0   1
  PTPRT MUTATED    26  54
  PTPRT WILD-TYPE  80 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     26   54
  PTPRT WILD-TYPE   80  116
        clus
vv       PTPRT MUTATED PTPRT WILD-TYPE
  FEMALE            26              80
  MALE              54             116
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPRT MUTATED       0                         0    80
  PTPRT WILD-TYPE     3                         1   192
D83V13, multiclass
                           clus
vv                          PTPRT MUTATED PTPRT WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                80             192
[1] 3 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  79
  PTPRT WILD-TYPE   2 190
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED      1   79
  PTPRT WILD-TYPE    2  190
                        clus
vv                       PTPRT MUTATED PTPRT WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            79             190
[1] 2 2
[1] FALSE

Clustering(84) Variable = SELPLG MUTATION ANALYSIS
D84V1, survival
                  sevent
clus2                0   1
  SELPLG MUTATED     5   5
  SELPLG WILD-TYPE 121 135
  SELPLG MUTATED SELPLG WILD-TYPE 
              10              256 
  SELPLG MUTATED SELPLG WILD-TYPE 
               5              135 
$`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        36.33 
TCGA-EE-A2MC TCGA-EE-A3JD TCGA-ER-A19D TCGA-RP-A694 
       47.51        27.35         3.52         0.69 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        7.99        37.97        11.15        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        0.95        18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       12.16        14.70         5.79         0.33 

  SELPLG MUTATED SELPLG WILD-TYPE 
            0.69             0.13 
  SELPLG MUTATED SELPLG WILD-TYPE 
          103.59           125.65 
  SELPLG MUTATED SELPLG WILD-TYPE 
          26.860           16.355 
[1] "0.7 - 103.6 (26.9)" "0.1 - 125.7 (16.4)"
[1] "hr=" "1.1"
D84V2, survival
                  sevent
clus2                0   1
  SELPLG MUTATED     5   5
  SELPLG WILD-TYPE 124 136
  SELPLG MUTATED SELPLG WILD-TYPE 
              10              260 
  SELPLG MUTATED SELPLG WILD-TYPE 
               5              136 
$`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        86.14 
TCGA-EE-A2MC TCGA-EE-A3JD TCGA-ER-A19D TCGA-RP-A694 
       61.51        27.35        12.59         0.69 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       135.75       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
      151.27        91.56       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        63.78        72.07        64.64         2.60        56.84 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF 
      129.27        28.83        19.76        47.28       103.27       268.73 
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       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F 
        9.17        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-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 TCGA-RP-A693 
        6.67         0.33 

  SELPLG MUTATED SELPLG WILD-TYPE 
            0.69             0.16 
  SELPLG MUTATED SELPLG WILD-TYPE 
          137.92           357.37 
  SELPLG MUTATED SELPLG WILD-TYPE 
          50.630           51.815 
[1] "0.7 - 137.9 (50.6)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.2"
D84V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  SELPLG MUTATED                    3             0
  SELPLG WILD-TYPE                 36             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SELPLG MUTATED                                           2
  SELPLG WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  SELPLG MUTATED                     5
  SELPLG WILD-TYPE                 166
D84V4, multiclass
                                           clus
vv                                          SELPLG MUTATED SELPLG WILD-TYPE
  DISTANT METASTASIS                                     3               36
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                    5              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
  SELPLG MUTATED             0       0       1        1        1        2
  SELPLG WILD-TYPE          10       6      23        9       23       14
                  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        30         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  SELPLG MUTATED            0          0        1
  SELPLG WILD-TYPE         23         46       15
D84V5, multiclass
             clus
vv            SELPLG MUTATED SELPLG WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 1                9
  STAGE IB                 1               23
  STAGE II                 2               14
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               1               12
  STAGE IIIB               0               23
  STAGE IIIC               0               46
  STAGE IV                 1               15
[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    50 57 51 56
D84V6, multiclass
       clus
vv      SELPLG MUTATED SELPLG WILD-TYPE
  T0+T1              2               50
  T2                 2               57
  T3                 3               51
  T4                 1               56
[1] 4 2
[1] TRUE
[1] "dimension of 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 133  47  31  36
D84V7, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  N0              6              133
  N1              1               47
  N2              2               31
  N3              0               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                M0  M1 M1A M1B M1C
  SELPLG MUTATED     9   0   0   0   1
  SELPLG WILD-TYPE 235   4   3   2   7
D84V8, multiclass
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  M0               9              235
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 99 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      4    1
  SELPLG WILD-TYPE   99   67
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  NO               4               99
  YES              1               67
[1] 2 2
[1] FALSE
D84V10, binary
                  cls
clus                 0   1
  SELPLG MUTATED     3   7
  SELPLG WILD-TYPE  33 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      3    7
  SELPLG WILD-TYPE   33  232
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  NO               3               33
  YES              7              232
[1] 2 2
[1] FALSE
D84V11, continuous
D84V12, binary
                  cls
clus                 0   1
  SELPLG MUTATED     2   8
  SELPLG WILD-TYPE 104 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      2    8
  SELPLG WILD-TYPE  104  162
        clus
vv       SELPLG MUTATED SELPLG WILD-TYPE
  FEMALE              2              104
  MALE                8              162
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SELPLG MUTATED       0                         0    10
  SELPLG WILD-TYPE     3                         1   262
D84V13, multiclass
                           clus
vv                          SELPLG MUTATED SELPLG WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 10              262
[1] 3 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  10
  SELPLG WILD-TYPE   3 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      0   10
  SELPLG WILD-TYPE    3  259
                        clus
vv                       SELPLG MUTATED SELPLG WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              259
[1] 2 2
[1] FALSE

Clustering(85) Variable = CSN3 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  CSN3 MUTATED     4   0
  CSN3 WILD-TYPE 122 140
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            262 
  CSN3 MUTATED CSN3 WILD-TYPE 
             0            140 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO 
       54.31        32.28        21.44        32.61        25.78        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71         5.62        85.74        15.72        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-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15         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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  CSN3 MUTATED CSN3 WILD-TYPE 
         18.41           0.13 
  CSN3 MUTATED CSN3 WILD-TYPE 
         98.27         125.65 
  CSN3 MUTATED CSN3 WILD-TYPE 
        46.325         16.190 
[1] "18.4 - 98.3 (46.3)" "0.1 - 125.7 (16.2)"
[1] "hr="     "9300000"
D85V2, survival
                sevent
clus2              0   1
  CSN3 MUTATED     4   0
  CSN3 WILD-TYPE 125 141
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            266 
  CSN3 MUTATED CSN3 WILD-TYPE 
             0            141 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO 
      145.12        32.94        22.62        63.81        26.89       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  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         51.120 
[1] "53.2 - 135.8 (111.1)" "0.2 - 357.4 (51.1)"  
[1] "hr="     "9200000"
D85V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  CSN3 MUTATED                    1             0
  CSN3 WILD-TYPE                 38             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CSN3 MUTATED                                           0                   3
  CSN3 WILD-TYPE                                        60                 168
D85V4, multiclass
                                           clus
vv                                          CSN3 MUTATED CSN3 WILD-TYPE
  DISTANT METASTASIS                                   1             38
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            0             60
  REGIONAL LYMPH NODE                                  3            168
[1] 4 2
[1] 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      22       10       23       16
                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        31         13         23
                vv
clus             STAGE IIIC STAGE IV
  CSN3 MUTATED            0        0
  CSN3 WILD-TYPE         46       16
D85V5, multiclass
             clus
vv            CSN3 MUTATED CSN3 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                2             22
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               0             16
  STAGE IIA              0             10
  STAGE IIB              0             14
  STAGE IIC              0              9
  STAGE III              1             31
  STAGE IIIA             0             13
  STAGE IIIB             0             23
  STAGE IIIC             0             46
  STAGE IV               0             16
[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    50 57 54 57
D85V6, multiclass
       clus
vv      CSN3 MUTATED CSN3 WILD-TYPE
  T0+T1            2             50
  T2               2             57
  T3               0             54
  T4               0             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CSN3 MUTATED     3   1   0   0
  CSN3 WILD-TYPE 136  47  33  36
D85V7, multiclass
    clus
vv   CSN3 MUTATED CSN3 WILD-TYPE
  N0            3            136
  N1            1             47
  N2            0             33
  N3            0             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              M0  M1 M1A M1B M1C
  CSN3 MUTATED     4   0   0   0   0
  CSN3 WILD-TYPE 240   4   3   2   8
D85V8, multiclass
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  M0             4            240
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 101  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      2    0
  CSN3 WILD-TYPE  101   68
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  NO             2            101
  YES            0             68
[1] 2 2
[1] FALSE
D85V10, binary
                cls
clus               0   1
  CSN3 MUTATED     0   4
  CSN3 WILD-TYPE  36 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      0    4
  CSN3 WILD-TYPE   36  235
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  NO             0             36
  YES            4            235
[1] 2 2
[1] FALSE
D85V11, continuous
D85V12, binary
                cls
clus               0   1
  CSN3 MUTATED     1   3
  CSN3 WILD-TYPE 105 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      1    3
  CSN3 WILD-TYPE  105  167
        clus
vv       CSN3 MUTATED CSN3 WILD-TYPE
  FEMALE            1            105
  MALE              3            167
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSN3 MUTATED       0                         0     4
  CSN3 WILD-TYPE     3                         1   268
D85V13, multiclass
                           clus
vv                          CSN3 MUTATED CSN3 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                4            268
[1] 3 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   3 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      0    4
  CSN3 WILD-TYPE    3  265
                        clus
vv                       CSN3 MUTATED CSN3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            265
[1] 2 2
[1] FALSE

Clustering(86) Variable = SLC7A11 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                 0   1
  SLC7A11 MUTATED     7   3
  SLC7A11 WILD-TYPE 119 137
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               10               256 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
                3               137 
$`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        36.30        34.29         2.70 
TCGA-EE-A2MS TCGA-FW-A3R5 TCGA-GN-A266 TCGA-QB-A6FS 
       53.16         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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         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        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33         8.84        98.27         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         0.33         0.69 

  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
             0.99              0.13 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
            70.16            125.65 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
           23.755            16.900 
[1] "1.0 - 70.2 (23.8)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.8"
D86V2, survival
                   sevent
clus2                 0   1
  SLC7A11 MUTATED     7   3
  SLC7A11 WILD-TYPE 122 138
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
               10               260 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
                3               138 
$`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        36.82        67.43        28.83 
TCGA-EE-A2MS TCGA-FW-A3R5 TCGA-GN-A266 TCGA-QB-A6FS 
      162.48        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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        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        86.14        59.28       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
             6.67              0.16 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
           162.48            357.37 
  SLC7A11 MUTATED SLC7A11 WILD-TYPE 
           42.855            52.585 
[1] "6.7 - 162.5 (42.9)" "0.2 - 357.4 (52.6)"
[1] "hr=" "1.3"
D86V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC7A11 MUTATED                    1             1
  SLC7A11 WILD-TYPE                 38             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC7A11 MUTATED                                           2
  SLC7A11 WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  SLC7A11 MUTATED                     7
  SLC7A11 WILD-TYPE                 164
D86V4, multiclass
                                           clus
vv                                          SLC7A11 MUTATED SLC7A11 WILD-TYPE
  DISTANT METASTASIS                                      1                38
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                58
  REGIONAL LYMPH NODE                                     7               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
  SLC7A11 MUTATED             1       0       0        0        0        2
  SLC7A11 WILD-TYPE           9       6      24       10       24       14
                   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        30         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC7A11 MUTATED            1          2        0
  SLC7A11 WILD-TYPE         22         44       16
D86V5, multiclass
             clus
vv            SLC7A11 MUTATED SLC7A11 WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   0                24
  STAGE IA                  0                10
  STAGE IB                  0                24
  STAGE II                  2                14
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 0                 9
  STAGE III                 2                30
  STAGE IIIA                1                12
  STAGE IIIB                1                22
  STAGE IIIC                2                44
  STAGE IV                  0                16
[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    50 58 50 55
D86V6, multiclass
       clus
vv      SLC7A11 MUTATED SLC7A11 WILD-TYPE
  T0+T1               2                50
  T2                  1                58
  T3                  4                50
  T4                  2                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
  SLC7A11 MUTATED     4   3   2   1
  SLC7A11 WILD-TYPE 135  45  31  35
D86V7, multiclass
    clus
vv   SLC7A11 MUTATED SLC7A11 WILD-TYPE
  N0               4               135
  N1               3                45
  N2               2                31
  N3               1                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  SLC7A11 MUTATED    10   0   0   0   0
  SLC7A11 WILD-TYPE 234   4   3   2   8
D86V8, multiclass
     clus
vv    SLC7A11 MUTATED SLC7A11 WILD-TYPE
  M0               10               234
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 101  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      2    2
  SLC7A11 WILD-TYPE  101   66
     clus
vv    SLC7A11 MUTATED SLC7A11 WILD-TYPE
  NO                2               101
  YES               2                66
[1] 2 2
[1] FALSE
D86V10, binary
                   cls
clus                  0   1
  SLC7A11 MUTATED     3   8
  SLC7A11 WILD-TYPE  33 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      3    8
  SLC7A11 WILD-TYPE   33  231
     clus
vv    SLC7A11 MUTATED SLC7A11 WILD-TYPE
  NO                3                33
  YES               8               231
[1] 2 2
[1] FALSE
D86V11, continuous
D86V12, binary
                   cls
clus                  0   1
  SLC7A11 MUTATED     3   8
  SLC7A11 WILD-TYPE 103 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      3    8
  SLC7A11 WILD-TYPE  103  162
        clus
vv       SLC7A11 MUTATED SLC7A11 WILD-TYPE
  FEMALE               3               103
  MALE                 8               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC7A11 MUTATED       0                         0    11
  SLC7A11 WILD-TYPE     3                         1   261
D86V13, multiclass
                           clus
vv                          SLC7A11 MUTATED SLC7A11 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  11               261
[1] 3 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   3 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A11 MUTATED      0   11
  SLC7A11 WILD-TYPE    3  258
                        clus
vv                       SLC7A11 MUTATED SLC7A11 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              11               258
[1] 2 2
[1] FALSE

Clustering(87) Variable = SYNE1 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2               0   1
  SYNE1 MUTATED    34  36
  SYNE1 WILD-TYPE  92 104
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             70             196 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             36             104 
$`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        32.28        25.78         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        23.15         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        62.79         1.08        36.30 
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-A2MF TCGA-EE-A2MI 
       55.69         1.15         8.84        47.51         2.73        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
       63.42       125.65        21.60        60.49        53.16       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD 
      122.73        30.15        13.81        15.95        22.22        27.35 
TCGA-EE-A3JI TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG 
       33.60        34.88        34.68        17.72        78.44        12.62 
TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZK 
       11.74        14.24         7.30         3.39        20.38        12.89 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A6C9 
        5.23         7.36         2.27         0.99         0.16        11.61 
TCGA-GN-A265 TCGA-GN-A266 TCGA-RP-A693 TCGA-RP-A694 
       84.72        10.13         0.33         0.69 

$`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        86.76        44.19         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        59.57       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 
       29.23        93.21        54.74        31.30        54.31        21.44 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.61        52.01        47.87        13.68        17.72        23.11 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        13.22        11.57        10.55         6.31 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       12.20         5.13         4.31        60.23        15.85         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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2GL 
        9.67        36.33        51.12        60.00        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       33.83         5.42        13.02        34.98        36.33        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-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
      111.91        56.02        25.08        26.99        52.67         5.56 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       51.62         3.68        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       21.60        16.14         0.95        18.41        21.73        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-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       13.45        28.60        42.84         9.57        36.07         6.58 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80         1.87         1.51        13.08         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-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-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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY 
       10.78         5.98         6.41         0.20         0.13        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        9.90         7.23         0.85        44.28        31.33        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       15.42        12.16        14.70         5.79 

  SYNE1 MUTATED SYNE1 WILD-TYPE 
           0.16            0.13 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         125.65          114.67 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         18.705          16.190 
[1] "0.2 - 125.7 (18.7)" "0.1 - 114.7 (16.2)"
[1] "hr=" "1.1"
D87V2, survival
                 sevent
clus2               0   1
  SYNE1 MUTATED    35  36
  SYNE1 WILD-TYPE  94 105
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             71             199 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             36             105 
$`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        32.94        26.89       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        68.25 
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        63.78         2.60 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       36.82        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-A2MF 
       75.48       126.81        14.30        21.67        61.51       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      204.66        96.23       158.63        43.23       134.40       162.48 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JA 
      124.31       122.73        54.51        13.81        23.47        53.19 
TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 
       27.35       148.08       152.35       162.08       148.18        79.99 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       31.27        32.05        20.91        27.72        48.85       357.37 
TCGA-FS-A1ZK TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV 
       23.93        27.02        66.67        77.88        22.92         0.16 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-RP-A693 TCGA-RP-A694 
       11.74        84.72        10.13         0.33         0.69 

$`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        86.76        62.07       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        59.57       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 
       45.30       174.84        55.73        56.35       145.12        22.62 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81       135.75       137.92       178.32        18.18       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        22.29         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        54.02        17.29        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 
      133.81        91.56       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        64.64        56.84        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       195.02 
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        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
      161.03        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        71.21        53.26        51.62         3.68       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      172.18       127.20        36.95        64.08        34.32       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58        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-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89        37.25         8.88        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       16.37       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
      202.65        28.08         7.79        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-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        28.73       174.84        12.43        26.73        49.45 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20        47.54        19.30         9.90         7.23         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      139.89       117.93        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS 
        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 
          53.19           51.62 
[1] "0.2 - 357.4 (53.2)" "0.2 - 268.9 (51.6)"
[1] "hr=" "1.2"
D87V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  SYNE1 MUTATED                   13             2
  SYNE1 WILD-TYPE                 26             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SYNE1 MUTATED                                          16                  42
  SYNE1 WILD-TYPE                                        44                 129
D87V4, multiclass
                                           clus
vv                                          SYNE1 MUTATED SYNE1 WILD-TYPE
  DISTANT METASTASIS                                   13              26
  PRIMARY TUMOR                                         2               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            16              44
  REGIONAL LYMPH NODE                                  42             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       6        3        1        6
  SYNE1 WILD-TYPE           8       4      18        7       23       10
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SYNE1 MUTATED           1         4         1        10          4          6
  SYNE1 WILD-TYPE         9        10         8        22          9         17
                 vv
clus              STAGE IIIC STAGE IV
  SYNE1 MUTATED           15        5
  SYNE1 WILD-TYPE         31       11
D87V5, multiclass
             clus
vv            SYNE1 MUTATED SYNE1 WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 2               4
  STAGE I                 6              18
  STAGE IA                3               7
  STAGE IB                1              23
  STAGE II                6              10
  STAGE IIA               1               9
  STAGE IIB               4              10
  STAGE IIC               1               8
  STAGE III              10              22
  STAGE IIIA              4               9
  STAGE IIIB              6              17
  STAGE IIIC             15              31
  STAGE IV                5              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
  SYNE1 MUTATED      12 12 11 18
  SYNE1 WILD-TYPE    40 47 43 39
D87V6, multiclass
       clus
vv      SYNE1 MUTATED SYNE1 WILD-TYPE
  T0+T1            12              40
  T2               12              47
  T3               11              43
  T4               18              39
[1] 4 2
[1] TRUE
[1] "dimension of 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    32   8  13  13
  SYNE1 WILD-TYPE 107  40  20  23
D87V7, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  N0            32             107
  N1             8              40
  N2            13              20
  N3            13              23
[1] 4 2
[1] 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    62   1   1   2   2
  SYNE1 WILD-TYPE 182   3   2   0   6
D87V8, multiclass
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  M0             62             182
  M1              1               3
  M1A             1               2
  M1B             2               0
  M1C             2               6
[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 79 53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     24   15
  SYNE1 WILD-TYPE   79   53
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  NO             24              79
  YES            15              53
[1] 2 2
[1] FALSE
D87V10, binary
                 cls
clus                0   1
  SYNE1 MUTATED    16  57
  SYNE1 WILD-TYPE  20 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     16   57
  SYNE1 WILD-TYPE   20  182
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  NO             16              20
  YES            57             182
[1] 2 2
[1] FALSE
D87V11, continuous
D87V12, binary
                 cls
clus                0   1
  SYNE1 MUTATED    23  50
  SYNE1 WILD-TYPE  83 120
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     23   50
  SYNE1 WILD-TYPE   83  120
        clus
vv       SYNE1 MUTATED SYNE1 WILD-TYPE
  FEMALE            23              83
  MALE              50             120
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYNE1 MUTATED       0                         0    73
  SYNE1 WILD-TYPE     3                         1   199
D87V13, multiclass
                           clus
vv                          SYNE1 MUTATED SYNE1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                73             199
[1] 3 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  70
  SYNE1 WILD-TYPE   1 199
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED      2   70
  SYNE1 WILD-TYPE    1  199
                        clus
vv                       SYNE1 MUTATED SYNE1 WILD-TYPE
  HISPANIC OR LATINO                 2               1
  NOT HISPANIC OR LATINO            70             199
[1] 2 2
[1] FALSE

Clustering(88) Variable = NFASC MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2               0   1
  NFASC MUTATED    10  12
  NFASC WILD-TYPE 116 128
  NFASC MUTATED NFASC WILD-TYPE 
             22             244 
  NFASC MUTATED NFASC WILD-TYPE 
             12             128 
$`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        60.49        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        44.28        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        86.76        11.41        44.19 
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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        30.15        13.81        12.72        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.72        64.47         3.45        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         7.30         3.39         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR 
        7.17        30.87        12.92        12.89        47.38         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-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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        0.85        11.61        31.33        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  NFASC MUTATED NFASC WILD-TYPE 
           0.99            0.13 
  NFASC MUTATED NFASC WILD-TYPE 
          84.72          125.65 
  NFASC MUTATED NFASC WILD-TYPE 
         23.865          16.355 
[1] "1.0 - 84.7 (23.9)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1"  
D88V2, survival
                 sevent
clus2               0   1
  NFASC MUTATED    10  12
  NFASC WILD-TYPE 119 129
  NFASC MUTATED NFASC WILD-TYPE 
             22             248 
  NFASC MUTATED NFASC WILD-TYPE 
             12             129 
$`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       134.40        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       139.89        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        86.76        11.87        62.07 
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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       135.75       178.32        18.18 
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 
       22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       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       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19       201.80        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98         6.77        92.98       174.21        15.72       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       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-A1ZH 
       48.85        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        23.93       101.26        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-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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  NFASC MUTATED NFASC WILD-TYPE 
          10.13            0.16 
  NFASC MUTATED NFASC WILD-TYPE 
         357.37          314.56 
  NFASC MUTATED NFASC WILD-TYPE 
         66.490          51.485 
[1] "10.1 - 357.4 (66.5)" "0.2 - 314.6 (51.5)" 
[1] "hr=" "1.4"
D88V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NFASC MUTATED                    5             0
  NFASC WILD-TYPE                 34             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NFASC MUTATED                                           9                   8
  NFASC WILD-TYPE                                        51                 163
D88V4, multiclass
                                           clus
vv                                          NFASC MUTATED NFASC WILD-TYPE
  DISTANT METASTASIS                                    5              34
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             9              51
  REGIONAL LYMPH NODE                                   8             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
  NFASC MUTATED             2       0       1        0        1        2
  NFASC WILD-TYPE           8       6      23       10       23       14
                 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        27         13         21
                 vv
clus              STAGE IIIC STAGE IV
  NFASC MUTATED            2        1
  NFASC WILD-TYPE         44       15
D88V5, multiclass
             clus
vv            NFASC MUTATED NFASC WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              14
  STAGE IIA               2               8
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              27
  STAGE IIIA              0              13
  STAGE IIIB              2              21
  STAGE IIIC              2              44
  STAGE IV                1              15
[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    47 57 48 55
D88V6, multiclass
       clus
vv      NFASC MUTATED NFASC WILD-TYPE
  T0+T1             5              47
  T2                2              57
  T3                6              48
  T4                2              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
  NFASC MUTATED    10   4   4   1
  NFASC WILD-TYPE 129  44  29  35
D88V7, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  N0            10             129
  N1             4              44
  N2             4              29
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NFASC MUTATED    18   0   1   0   0
  NFASC WILD-TYPE 226   4   2   2   8
D88V8, multiclass
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  M0             18             226
  M1              0               4
  M1A             1               2
  M1B             0               2
  M1C             0               8
[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 99 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      4    3
  NFASC WILD-TYPE   99   65
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO              4              99
  YES             3              65
[1] 2 2
[1] FALSE
D88V10, binary
                 cls
clus                0   1
  NFASC MUTATED     7  15
  NFASC WILD-TYPE  29 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      7   15
  NFASC WILD-TYPE   29  224
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO              7              29
  YES            15             224
[1] 2 2
[1] FALSE
D88V11, continuous
D88V12, binary
                 cls
clus                0   1
  NFASC MUTATED     6  16
  NFASC WILD-TYPE 100 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      6   16
  NFASC WILD-TYPE  100  154
        clus
vv       NFASC MUTATED NFASC WILD-TYPE
  FEMALE             6             100
  MALE              16             154
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFASC MUTATED       0                         0    22
  NFASC WILD-TYPE     3                         1   250
D88V13, multiclass
                           clus
vv                          NFASC MUTATED NFASC WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                22             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"
D88V14, binary
                 cls
clus                0   1
  NFASC MUTATED     1  21
  NFASC WILD-TYPE   2 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      1   21
  NFASC WILD-TYPE    2  248
                        clus
vv                       NFASC MUTATED NFASC WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            21             248
[1] 2 2
[1] FALSE

Clustering(89) Variable = CCDC11 MUTATION ANALYSIS
D89V1, survival
                  sevent
clus2                0   1
  CCDC11 MUTATED     7  10
  CCDC11 WILD-TYPE 119 130
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              249 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              130 
$`CCDC11 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A181 
       32.42        44.19         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        39.62        36.30        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        86.76        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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       17.72        23.11        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
       23.15        19.00        13.35        13.22        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        60.23 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         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        32.15 
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        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        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        55.69         5.42         1.15        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-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-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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  CCDC11 MUTATED CCDC11 WILD-TYPE 
            1.12             0.13 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           98.27           125.65 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           30.08            16.14 
[1] "1.1 - 98.3 (30.1)"  "0.1 - 125.7 (16.1)"
[1] "hr=" "1"  
D89V2, survival
                  sevent
clus2                0   1
  CCDC11 MUTATED     7  10
  CCDC11 WILD-TYPE 122 131
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              17              253 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              131 
$`CCDC11 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A181 
      112.57        62.07        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        56.84        36.82        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        86.76        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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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 
       22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
       17.29        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       133.81        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         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       195.02        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        86.14        59.28       314.56       161.03 
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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       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       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       10.13        64.44        62.79        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  CCDC11 MUTATED CCDC11 WILD-TYPE 
           11.34             0.16 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
          151.27           357.37 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           48.72            53.16 
[1] "11.3 - 151.3 (48.7)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1.4"
D89V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CCDC11 MUTATED                    2             0
  CCDC11 WILD-TYPE                 37             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CCDC11 MUTATED                                           4
  CCDC11 WILD-TYPE                                        56
                  vv
clus               REGIONAL LYMPH NODE
  CCDC11 MUTATED                    11
  CCDC11 WILD-TYPE                 160
D89V4, multiclass
                                           clus
vv                                          CCDC11 MUTATED CCDC11 WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              4               56
  REGIONAL LYMPH NODE                                   11              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
  CCDC11 MUTATED             1       1       1        3        2        1
  CCDC11 WILD-TYPE           9       5      23        7       22       15
                  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        29         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CCDC11 MUTATED            1          2        0
  CCDC11 WILD-TYPE         22         44       16
D89V5, multiclass
             clus
vv            CCDC11 MUTATED CCDC11 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  1                5
  STAGE I                  1               23
  STAGE IA                 3                7
  STAGE IB                 2               22
  STAGE II                 1               15
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                3               29
  STAGE IIIA               1               12
  STAGE IIIB               1               22
  STAGE IIIC               2               44
  STAGE IV                 0               16
[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    46 56 51 54
D89V6, multiclass
       clus
vv      CCDC11 MUTATED CCDC11 WILD-TYPE
  T0+T1              6               46
  T2                 3               56
  T3                 3               51
  T4                 3               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
  CCDC11 MUTATED    11   3   2   1
  CCDC11 WILD-TYPE 128  45  31  35
D89V7, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  N0             11              128
  N1              3               45
  N2              2               31
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  CCDC11 MUTATED    17   0   0   0   0
  CCDC11 WILD-TYPE 227   4   3   2   8
D89V8, multiclass
     clus
vv    CCDC11 MUTATED CCDC11 WILD-TYPE
  M0              17              227
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 94 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      9    2
  CCDC11 WILD-TYPE   94   66
     clus
vv    CCDC11 MUTATED CCDC11 WILD-TYPE
  NO               9               94
  YES              2               66
[1] 2 2
[1] FALSE
D89V10, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     2  15
  CCDC11 WILD-TYPE  34 224
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      2   15
  CCDC11 WILD-TYPE   34  224
     clus
vv    CCDC11 MUTATED CCDC11 WILD-TYPE
  NO               2               34
  YES             15              224
[1] 2 2
[1] FALSE
D89V11, continuous
D89V12, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     5  12
  CCDC11 WILD-TYPE 101 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      5   12
  CCDC11 WILD-TYPE  101  158
        clus
vv       CCDC11 MUTATED CCDC11 WILD-TYPE
  FEMALE              5              101
  MALE               12              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC11 MUTATED       0                         0    17
  CCDC11 WILD-TYPE     3                         1   255
D89V13, multiclass
                           clus
vv                          CCDC11 MUTATED CCDC11 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 17              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"
D89V14, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     0  16
  CCDC11 WILD-TYPE   3 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      0   16
  CCDC11 WILD-TYPE    3  253
                        clus
vv                       CCDC11 MUTATED CCDC11 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             16              253
[1] 2 2
[1] FALSE

Clustering(90) Variable = IL31RA MUTATION ANALYSIS
D90V1, survival
                  sevent
clus2                0   1
  IL31RA MUTATED    10   6
  IL31RA WILD-TYPE 116 134
  IL31RA MUTATED IL31RA WILD-TYPE 
              16              250 
  IL31RA MUTATED IL31RA WILD-TYPE 
               6              134 
$`IL31RA MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A181 TCGA-EE-A29M TCGA-EE-A2GT 
       85.32        44.19        13.22         1.12        39.62        34.98 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JI 
       26.99        52.67        51.62        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        86.76        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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         5.42         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       60.49        53.16         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14         0.95        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        52.08         8.65        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         0.82         5.23         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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         0.33         0.69 

  IL31RA MUTATED IL31RA WILD-TYPE 
            0.99             0.13 
  IL31RA MUTATED IL31RA WILD-TYPE 
           85.32           125.65 
  IL31RA MUTATED IL31RA WILD-TYPE 
          30.295           16.190 
[1] "1.0 - 85.3 (30.3)"  "0.1 - 125.7 (16.2)"
[1] "hr=" "1.6"
D90V2, survival
                  sevent
clus2                0   1
  IL31RA MUTATED    10   6
  IL31RA WILD-TYPE 119 135
  IL31RA MUTATED IL31RA WILD-TYPE 
              16              254 
  IL31RA MUTATED IL31RA WILD-TYPE 
               6              135 
$`IL31RA MUTATED`
TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A181 TCGA-EE-A29M TCGA-EE-A2GT 
      103.10        62.07        66.25        33.73        56.84        44.88 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JI 
      248.65        71.21        51.62        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        86.76        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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54        43.23       134.40       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31       122.73         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  IL31RA MUTATED IL31RA WILD-TYPE 
            6.67             0.16 
  IL31RA MUTATED IL31RA WILD-TYPE 
          248.65           357.37 
  IL31RA MUTATED IL31RA WILD-TYPE 
          55.015           51.120 
[1] "6.7 - 248.7 (55.0)" "0.2 - 357.4 (51.1)"
[1] "hr=" "1.4"
D90V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  IL31RA MUTATED                    2             1
  IL31RA WILD-TYPE                 37             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  IL31RA MUTATED                                           3
  IL31RA WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  IL31RA MUTATED                    11
  IL31RA WILD-TYPE                 160
D90V4, multiclass
                                           clus
vv                                          IL31RA MUTATED IL31RA WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              3               57
  REGIONAL LYMPH NODE                                   11              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
  IL31RA MUTATED             1       0       2        1        3        2
  IL31RA WILD-TYPE           9       6      22        9       21       14
                  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        29         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  IL31RA MUTATED            0          2        0
  IL31RA WILD-TYPE         23         44       16
D90V5, multiclass
             clus
vv            IL31RA MUTATED IL31RA WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  2               22
  STAGE IA                 1                9
  STAGE IB                 3               21
  STAGE II                 2               14
  STAGE IIA                1                9
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                3               29
  STAGE IIIA               1               12
  STAGE IIIB               0               23
  STAGE IIIC               2               44
  STAGE IV                 0               16
[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    48 52 50 56
D90V6, multiclass
       clus
vv      IL31RA MUTATED IL31RA WILD-TYPE
  T0+T1              4               48
  T2                 7               52
  T3                 4               50
  T4                 1               56
[1] 4 2
[1] TRUE
[1] "dimension of 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 128  46  30  35
D90V7, multiclass
    clus
vv   IL31RA MUTATED IL31RA WILD-TYPE
  N0             11              128
  N1              2               46
  N2              3               30
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  IL31RA MUTATED    17   0   0   0   0
  IL31RA WILD-TYPE 227   4   3   2   8
D90V8, multiclass
     clus
vv    IL31RA MUTATED IL31RA WILD-TYPE
  M0              17              227
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 95 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      8    1
  IL31RA WILD-TYPE   95   67
     clus
vv    IL31RA MUTATED IL31RA WILD-TYPE
  NO               8               95
  YES              1               67
[1] 2 2
[1] FALSE
D90V10, binary
                  cls
clus                 0   1
  IL31RA MUTATED     3  14
  IL31RA WILD-TYPE  33 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      3   14
  IL31RA WILD-TYPE   33  225
     clus
vv    IL31RA MUTATED IL31RA WILD-TYPE
  NO               3               33
  YES             14              225
[1] 2 2
[1] FALSE
D90V11, continuous
D90V12, binary
                  cls
clus                 0   1
  IL31RA MUTATED     6  11
  IL31RA WILD-TYPE 100 159
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      6   11
  IL31RA WILD-TYPE  100  159
        clus
vv       IL31RA MUTATED IL31RA WILD-TYPE
  FEMALE              6              100
  MALE               11              159
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL31RA MUTATED       0                         0    17
  IL31RA WILD-TYPE     3                         1   255
D90V13, multiclass
                           clus
vv                          IL31RA MUTATED IL31RA WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 17              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"
D90V14, binary
                  cls
clus                 0   1
  IL31RA MUTATED     0  17
  IL31RA WILD-TYPE   3 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL31RA MUTATED      0   17
  IL31RA WILD-TYPE    3  252
                        clus
vv                       IL31RA MUTATED IL31RA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             17              252
[1] 2 2
[1] FALSE

Clustering(91) Variable = MLL MUTATION ANALYSIS
D91V1, survival
               sevent
clus2             0   1
  MLL MUTATED    20  17
  MLL WILD-TYPE 106 123
  MLL MUTATED MLL WILD-TYPE 
           37           229 
  MLL MUTATED MLL WILD-TYPE 
           17           123 
$`MLL MUTATED`
TCGA-D3-A1QA TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 
       45.83        46.98        25.78         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        36.30 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AF 
       34.29        30.08        33.83        60.49       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-GF-A6C9 
       49.15        27.39         5.23         0.99         0.13        11.61 
TCGA-GN-A26D 
       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        86.76        11.41        44.19 
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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       23.11        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         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        36.33        51.12        17.98        60.00        47.21 
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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
        5.56       122.73        51.62         3.68        30.15        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       12.72         3.22        21.60         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       21.73        33.60        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       34.68         9.57         6.58        17.72        78.44         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
        1.51        13.08        12.62        11.74         9.04        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX 
        1.71         5.62        18.41        85.74        15.72         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-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-A1ZT TCGA-FS-A1ZU 
       47.38        52.08         8.65         8.81        40.64         8.68 
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-A3TV TCGA-FW-A5DY 
        5.98         6.41         2.27         0.20         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-QB-A6FS TCGA-RP-A693 
       10.13        16.24        15.42        12.16         5.79         0.33 
TCGA-RP-A694 
        0.69 

  MLL MUTATED MLL WILD-TYPE 
         0.13          0.16 
  MLL MUTATED MLL WILD-TYPE 
       124.31        125.65 
  MLL MUTATED MLL WILD-TYPE 
        22.22         16.01 
[1] "0.1 - 124.3 (22.2)" "0.2 - 125.7 (16.0)"
[1] "hr=" "1.2"
D91V2, survival
               sevent
clus2             0   1
  MLL MUTATED    20  17
  MLL WILD-TYPE 109 124
  MLL MUTATED MLL WILD-TYPE 
           37           233 
  MLL MUTATED MLL WILD-TYPE 
           17           124 
$`MLL MUTATED`
TCGA-D3-A1QA TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 
       90.90        46.98        26.89        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        36.82 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AF 
       67.43        48.72        90.97       134.40       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-GF-A6C9 
      148.80        49.48        27.02        22.92        47.54        11.74 
TCGA-GN-A26D 
       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        86.76        11.87        62.07 
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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81       135.75       137.92       178.32        18.18 
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        22.29 
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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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 
      195.02        17.92        46.82       102.90        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       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       162.48        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        54.51        23.47       138.81       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08       201.80        27.35        51.35       109.58       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18        79.99        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       31.27        32.05       247.04        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       92.98       174.21        15.72        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-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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
      133.55        11.41        53.16        26.56        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       77.88         0.20         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48         6.67         0.33         0.69 

  MLL MUTATED MLL WILD-TYPE 
        11.34          0.16 
  MLL MUTATED MLL WILD-TYPE 
       357.37        314.56 
  MLL MUTATED MLL WILD-TYPE 
        43.82         53.92 
[1] "11.3 - 357.4 (43.8)" "0.2 - 314.6 (53.9)" 
[1] "hr=" "1.2"
D91V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  MLL MUTATED                    9             0
  MLL WILD-TYPE                 30             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MLL MUTATED                                           7                  22
  MLL WILD-TYPE                                        53                 149
D91V4, multiclass
                                           clus
vv                                          MLL MUTATED MLL WILD-TYPE
  DISTANT METASTASIS                                  9            30
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           7            53
  REGIONAL LYMPH NODE                                22           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
  MLL MUTATED             2       0       2        1        4        2
  MLL WILD-TYPE           8       6      22        9       20       14
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MLL MUTATED           1         3         1         4          2          5
  MLL WILD-TYPE         9        11         8        28         11         18
               vv
clus            STAGE IIIC STAGE IV
  MLL MUTATED            6        3
  MLL WILD-TYPE         40       13
D91V5, multiclass
             clus
vv            MLL MUTATED MLL WILD-TYPE
  I OR II NOS           2             8
  STAGE 0               0             6
  STAGE I               2            22
  STAGE IA              1             9
  STAGE IB              4            20
  STAGE II              2            14
  STAGE IIA             1             9
  STAGE IIB             3            11
  STAGE IIC             1             8
  STAGE III             4            28
  STAGE IIIA            2            11
  STAGE IIIB            5            18
  STAGE IIIC            6            40
  STAGE IV              3            13
[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    45 49 47 50
D91V6, multiclass
       clus
vv      MLL MUTATED MLL WILD-TYPE
  T0+T1           7            45
  T2             10            49
  T3              7            47
  T4              7            50
[1] 4 2
[1] TRUE
[1] "dimension of 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   8   5   4
  MLL WILD-TYPE 121  40  28  32
D91V7, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  N0          18           121
  N1           8            40
  N2           5            28
  N3           4            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
  MLL MUTATED    31   1   1   0   1
  MLL WILD-TYPE 213   3   2   2   7
D91V8, multiclass
     clus
vv    MLL MUTATED MLL WILD-TYPE
  M0           31           213
  M1            1             3
  M1A           1             2
  M1B           0             2
  M1C           1             7
[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 92 56
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     11   12
  MLL WILD-TYPE   92   56
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO           11            92
  YES          12            56
[1] 2 2
[1] FALSE
D91V10, binary
               cls
clus              0   1
  MLL MUTATED     7  31
  MLL WILD-TYPE  29 208
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      7   31
  MLL WILD-TYPE   29  208
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO            7            29
  YES          31           208
[1] 2 2
[1] FALSE
D91V11, continuous
D91V12, binary
               cls
clus              0   1
  MLL MUTATED    13  25
  MLL WILD-TYPE  93 145
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     13   25
  MLL WILD-TYPE   93  145
        clus
vv       MLL MUTATED MLL WILD-TYPE
  FEMALE          13            93
  MALE            25           145
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL MUTATED       0                         0    38
  MLL WILD-TYPE     3                         1   234
D91V13, multiclass
                           clus
vv                          MLL MUTATED MLL WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              38           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"
D91V14, binary
               cls
clus              0   1
  MLL MUTATED     1  37
  MLL WILD-TYPE   2 232
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      1   37
  MLL WILD-TYPE    2  232
                        clus
vv                       MLL MUTATED MLL WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          37           232
[1] 2 2
[1] FALSE

Clustering(92) Variable = DIRC2 MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2               0   1
  DIRC2 MUTATED     1   3
  DIRC2 WILD-TYPE 125 137
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             262 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              3             137 
$`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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       98.27         2.70        47.51         9.53        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  DIRC2 MUTATED DIRC2 WILD-TYPE 
           0.99            0.13 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
           8.52          125.65 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
           5.80           17.64 
[1] "1.0 - 8.5 (5.8)"    "0.1 - 125.7 (17.6)"
[1] "hr=" "7.2"
D92V2, survival
                 sevent
clus2               0   1
  DIRC2 MUTATED     1   3
  DIRC2 WILD-TYPE 128 138
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              4             266 
  DIRC2 MUTATED DIRC2 WILD-TYPE 
              3             138 
$`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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  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          53.175 
[1] "13.9 - 22.9 (18.2)" "0.2 - 357.4 (53.2)"
[1] "hr=" "6"  
D92V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DIRC2 MUTATED                    0             0
  DIRC2 WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DIRC2 MUTATED                                           1                   3
  DIRC2 WILD-TYPE                                        59                 168
D92V4, multiclass
                                           clus
vv                                          DIRC2 MUTATED DIRC2 WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                   3             168
[1] 4 2
[1] 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      24       10       24       16
                 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        30         13         22
                 vv
clus              STAGE IIIC STAGE IV
  DIRC2 MUTATED            0        0
  DIRC2 WILD-TYPE         46       16
D92V5, multiclass
             clus
vv            DIRC2 MUTATED DIRC2 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               2              30
  STAGE IIIA              0              13
  STAGE IIIB              1              22
  STAGE IIIC              0              46
  STAGE IV                0              16
[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    52 59 53 55
D92V6, multiclass
       clus
vv      DIRC2 MUTATED DIRC2 WILD-TYPE
  T0+T1             0              52
  T2                0              59
  T3                1              53
  T4                2              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
  DIRC2 MUTATED     1   2   1   0
  DIRC2 WILD-TYPE 138  46  32  36
D92V7, multiclass
    clus
vv   DIRC2 MUTATED DIRC2 WILD-TYPE
  N0             1             138
  N1             2              46
  N2             1              32
  N3             0              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               M0  M1 M1A M1B M1C
  DIRC2 MUTATED     4   0   0   0   0
  DIRC2 WILD-TYPE 240   4   3   2   8
D92V8, multiclass
     clus
vv    DIRC2 MUTATED DIRC2 WILD-TYPE
  M0              4             240
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 102  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      1    2
  DIRC2 WILD-TYPE  102   66
     clus
vv    DIRC2 MUTATED DIRC2 WILD-TYPE
  NO              1             102
  YES             2              66
[1] 2 2
[1] FALSE
D92V10, binary
                 cls
clus                0   1
  DIRC2 MUTATED     0   4
  DIRC2 WILD-TYPE  36 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      0    4
  DIRC2 WILD-TYPE   36  235
     clus
vv    DIRC2 MUTATED DIRC2 WILD-TYPE
  NO              0              36
  YES             4             235
[1] 2 2
[1] FALSE
D92V11, continuous
D92V12, binary
                 cls
clus                0   1
  DIRC2 MUTATED     1   3
  DIRC2 WILD-TYPE 105 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      1    3
  DIRC2 WILD-TYPE  105  167
        clus
vv       DIRC2 MUTATED DIRC2 WILD-TYPE
  FEMALE             1             105
  MALE               3             167
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DIRC2 MUTATED       0                         0     4
  DIRC2 WILD-TYPE     3                         1   268
D92V13, multiclass
                           clus
vv                          DIRC2 MUTATED DIRC2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 4             268
[1] 3 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   3 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIRC2 MUTATED      0    4
  DIRC2 WILD-TYPE    3  265
                        clus
vv                       DIRC2 MUTATED DIRC2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             265
[1] 2 2
[1] FALSE

Clustering(93) Variable = ADAM22 MUTATION ANALYSIS
D93V1, survival
                  sevent
clus2                0   1
  ADAM22 MUTATED    11   8
  ADAM22 WILD-TYPE 115 132
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              247 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
               8              132 
$`ADAM22 MUTATED`
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D9-A6EC TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
      103.59        93.21        13.22        37.97        36.85        39.62 
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         0.85        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        11.15        62.79         8.55 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W 
        1.08        12.03         8.09         8.84         9.99        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       51.12        34.29        17.98        60.00        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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
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-A19F TCGA-ER-A19G 
       76.41        25.18         3.78         3.52        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-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-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.39         0.82        53.85        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-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       17.33         9.90         7.23        11.61        44.28        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  ADAM22 MUTATED ADAM22 WILD-TYPE 
            0.85             0.13 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
          103.59           125.65 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
           11.90            17.56 
[1] "0.8 - 103.6 (11.9)" "0.1 - 125.7 (17.6)"
[1] "hr=" "1.2"
D93V2, survival
                  sevent
clus2                0   1
  ADAM22 MUTATED    11   8
  ADAM22 WILD-TYPE 118 133
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              19              251 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
               8              133 
$`ADAM22 MUTATED`
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D9-A6EC TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
      103.59       174.84        66.25        47.84        64.64        56.84 
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         2.04        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      248.65        43.23       134.40       162.48        71.21       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-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-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        7.23        11.74       139.89       117.93        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  ADAM22 MUTATED ADAM22 WILD-TYPE 
            2.04             0.16 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
          174.84           357.37 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
           48.72            52.01 
[1] "2.0 - 174.8 (48.7)" "0.2 - 357.4 (52.0)"
[1] "hr=" "1"  
D93V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ADAM22 MUTATED                    3             1
  ADAM22 WILD-TYPE                 36             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ADAM22 MUTATED                                           6
  ADAM22 WILD-TYPE                                        54
                  vv
clus               REGIONAL LYMPH NODE
  ADAM22 MUTATED                     9
  ADAM22 WILD-TYPE                 162
D93V4, multiclass
                                           clus
vv                                          ADAM22 MUTATED ADAM22 WILD-TYPE
  DISTANT METASTASIS                                     3               36
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              6               54
  REGIONAL LYMPH NODE                                    9              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
  ADAM22 MUTATED             3       0       0        3        3        0
  ADAM22 WILD-TYPE           7       6      24        7       21       16
                  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        29         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ADAM22 MUTATED            0          1        0
  ADAM22 WILD-TYPE         23         45       16
D93V5, multiclass
             clus
vv            ADAM22 MUTATED ADAM22 WILD-TYPE
  I OR II NOS              3                7
  STAGE 0                  0                6
  STAGE I                  0               24
  STAGE IA                 3                7
  STAGE IB                 3               21
  STAGE II                 0               16
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                3               29
  STAGE IIIA               1               12
  STAGE IIIB               0               23
  STAGE IIIC               1               45
  STAGE IV                 0               16
[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    48 54 50 56
D93V6, multiclass
       clus
vv      ADAM22 MUTATED ADAM22 WILD-TYPE
  T0+T1              4               48
  T2                 5               54
  T3                 4               50
  T4                 1               56
[1] 4 2
[1] TRUE
[1] "dimension of 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 128  44  32  36
D93V7, multiclass
    clus
vv   ADAM22 MUTATED ADAM22 WILD-TYPE
  N0             11              128
  N1              4               44
  N2              1               32
  N3              0               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                M0  M1 M1A M1B M1C
  ADAM22 MUTATED    17   0   0   0   0
  ADAM22 WILD-TYPE 227   4   3   2   8
D93V8, multiclass
     clus
vv    ADAM22 MUTATED ADAM22 WILD-TYPE
  M0              17              227
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 95 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      8    4
  ADAM22 WILD-TYPE   95   64
     clus
vv    ADAM22 MUTATED ADAM22 WILD-TYPE
  NO               8               95
  YES              4               64
[1] 2 2
[1] FALSE
D93V10, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     3  16
  ADAM22 WILD-TYPE  33 223
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      3   16
  ADAM22 WILD-TYPE   33  223
     clus
vv    ADAM22 MUTATED ADAM22 WILD-TYPE
  NO               3               33
  YES             16              223
[1] 2 2
[1] FALSE
D93V11, continuous
D93V12, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     7  12
  ADAM22 WILD-TYPE  99 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      7   12
  ADAM22 WILD-TYPE   99  158
        clus
vv       ADAM22 MUTATED ADAM22 WILD-TYPE
  FEMALE              7               99
  MALE               12              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM22 MUTATED       0                         0    19
  ADAM22 WILD-TYPE     3                         1   253
D93V13, multiclass
                           clus
vv                          ADAM22 MUTATED ADAM22 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 19              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"
D93V14, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     1  17
  ADAM22 WILD-TYPE   2 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      1   17
  ADAM22 WILD-TYPE    2  252
                        clus
vv                       ADAM22 MUTATED ADAM22 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             17              252
[1] 2 2
[1] FALSE

Clustering(94) Variable = PLCXD2 MUTATION ANALYSIS
D94V1, survival
                  sevent
clus2                0   1
  PLCXD2 MUTATED     3   5
  PLCXD2 WILD-TYPE 123 135
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               8              258 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               5              135 
$`PLCXD2 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EA TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A3AH 
       44.19        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        86.76        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69 
TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        5.42        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       15.95        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
            0.99             0.13 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
           44.19           125.65 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
           10.42            17.72 
[1] "1.0 - 44.2 (10.4)"  "0.1 - 125.7 (17.7)"
[1] "hr=" "2.2"
D94V2, survival
                  sevent
clus2                0   1
  PLCXD2 MUTATED     3   5
  PLCXD2 WILD-TYPE 126 136
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               8              262 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
               5              136 
$`PLCXD2 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EA TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A3AH 
       62.07        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        86.76        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 
       51.62         3.68        54.51        13.81        23.47       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
           14.30             0.16 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
          172.18           357.37 
  PLCXD2 MUTATED PLCXD2 WILD-TYPE 
          51.435           51.815 
[1] "14.3 - 172.2 (51.4)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1.3"
D94V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PLCXD2 MUTATED                    2             1
  PLCXD2 WILD-TYPE                 37             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PLCXD2 MUTATED                                           3
  PLCXD2 WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  PLCXD2 MUTATED                     3
  PLCXD2 WILD-TYPE                 168
D94V4, multiclass
                                           clus
vv                                          PLCXD2 MUTATED PLCXD2 WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              3               57
  REGIONAL LYMPH NODE                                    3              168
[1] 4 2
[1] 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      24        9       22       13
                  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        31         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PLCXD2 MUTATED            0          1        0
  PLCXD2 WILD-TYPE         23         45       16
D94V5, multiclass
             clus
vv            PLCXD2 MUTATED PLCXD2 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  0               24
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 3               13
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               31
  STAGE IIIA               0               13
  STAGE IIIB               0               23
  STAGE IIIC               1               45
  STAGE IV                 0               16
[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    51 56 52 55
D94V6, multiclass
       clus
vv      PLCXD2 MUTATED PLCXD2 WILD-TYPE
  T0+T1              1               51
  T2                 3               56
  T3                 2               52
  T4                 2               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
  PLCXD2 MUTATED     7   0   1   1
  PLCXD2 WILD-TYPE 132  48  32  35
D94V7, multiclass
    clus
vv   PLCXD2 MUTATED PLCXD2 WILD-TYPE
  N0              7              132
  N1              0               48
  N2              1               32
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  PLCXD2 MUTATED     9   0   0   0   0
  PLCXD2 WILD-TYPE 235   4   3   2   8
D94V8, multiclass
     clus
vv    PLCXD2 MUTATED PLCXD2 WILD-TYPE
  M0               9              235
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 99 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      4    1
  PLCXD2 WILD-TYPE   99   67
     clus
vv    PLCXD2 MUTATED PLCXD2 WILD-TYPE
  NO               4               99
  YES              1               67
[1] 2 2
[1] FALSE
D94V10, binary
                  cls
clus                 0   1
  PLCXD2 MUTATED     0   9
  PLCXD2 WILD-TYPE  36 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      0    9
  PLCXD2 WILD-TYPE   36  230
     clus
vv    PLCXD2 MUTATED PLCXD2 WILD-TYPE
  NO               0               36
  YES              9              230
[1] 2 2
[1] FALSE
D94V11, continuous
D94V12, binary
                  cls
clus                 0   1
  PLCXD2 MUTATED     2   7
  PLCXD2 WILD-TYPE 104 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      2    7
  PLCXD2 WILD-TYPE  104  163
        clus
vv       PLCXD2 MUTATED PLCXD2 WILD-TYPE
  FEMALE              2              104
  MALE                7              163
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLCXD2 MUTATED       0                         0     9
  PLCXD2 WILD-TYPE     3                         1   263
D94V13, multiclass
                           clus
vv                          PLCXD2 MUTATED PLCXD2 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  9              263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V14, binary
                  cls
clus                 0   1
  PLCXD2 MUTATED     0   9
  PLCXD2 WILD-TYPE   3 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLCXD2 MUTATED      0    9
  PLCXD2 WILD-TYPE    3  260
                        clus
vv                       PLCXD2 MUTATED PLCXD2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              9              260
[1] 2 2
[1] FALSE

Clustering(95) Variable = EDN1 MUTATION ANALYSIS
D95V1, survival
                sevent
clus2              0   1
  EDN1 MUTATED     4   5
  EDN1 WILD-TYPE 122 135
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            257 
  EDN1 MUTATED EDN1 WILD-TYPE 
             5            135 
$`EDN1 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2J9 TCGA-D3-A51T TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       32.42        21.14        25.78         8.12        11.15        36.33 
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-GN-A266 
       60.49         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        86.76        11.41        44.19         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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  EDN1 MUTATED EDN1 WILD-TYPE 
          0.99           0.13 
  EDN1 MUTATED EDN1 WILD-TYPE 
         60.49         125.65 
  EDN1 MUTATED EDN1 WILD-TYPE 
         21.14          16.47 
[1] "1.0 - 60.5 (21.1)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.1"
D95V2, survival
                sevent
clus2              0   1
  EDN1 MUTATED     4   5
  EDN1 WILD-TYPE 125 136
  EDN1 MUTATED EDN1 WILD-TYPE 
             9            261 
  EDN1 MUTATED EDN1 WILD-TYPE 
             5            136 
$`EDN1 MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2J9 TCGA-D3-A51T TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
      112.57        23.77        26.89        94.98        13.97        86.14 
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-GN-A266 
      134.40        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        86.76        11.87        62.07       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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60        56.84 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  EDN1 MUTATED EDN1 WILD-TYPE 
         10.13           0.16 
  EDN1 MUTATED EDN1 WILD-TYPE 
        134.40         357.37 
  EDN1 MUTATED EDN1 WILD-TYPE 
         26.89          52.01 
[1] "10.1 - 134.4 (26.9)" "0.2 - 357.4 (52.0)" 
[1] "hr=" "1.4"
D95V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  EDN1 MUTATED                    1             0
  EDN1 WILD-TYPE                 38             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  EDN1 MUTATED                                           1                   7
  EDN1 WILD-TYPE                                        59                 164
D95V4, multiclass
                                           clus
vv                                          EDN1 MUTATED EDN1 WILD-TYPE
  DISTANT METASTASIS                                   1             38
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            1             59
  REGIONAL LYMPH NODE                                  7            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
  EDN1 MUTATED             1       0       1        1        0        0
  EDN1 WILD-TYPE           9       6      23        9       24       16
                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        30         13         23
                vv
clus             STAGE IIIC STAGE IV
  EDN1 MUTATED            3        0
  EDN1 WILD-TYPE         43       16
D95V5, multiclass
             clus
vv            EDN1 MUTATED EDN1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                1             23
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               0             16
  STAGE IIA              0             10
  STAGE IIB              0             14
  STAGE IIC              0              9
  STAGE III              2             30
  STAGE IIIA             0             13
  STAGE IIIB             0             23
  STAGE IIIC             3             43
  STAGE IV               0             16
[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    51 58 53 54
D95V6, multiclass
       clus
vv      EDN1 MUTATED EDN1 WILD-TYPE
  T0+T1            1             51
  T2               1             58
  T3               1             53
  T4               3             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
  EDN1 MUTATED     4   2   1   1
  EDN1 WILD-TYPE 135  46  32  35
D95V7, multiclass
    clus
vv   EDN1 MUTATED EDN1 WILD-TYPE
  N0            4            135
  N1            2             46
  N2            1             32
  N3            1             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  EDN1 MUTATED     8   0   0   0   0
  EDN1 WILD-TYPE 236   4   3   2   8
D95V8, multiclass
     clus
vv    EDN1 MUTATED EDN1 WILD-TYPE
  M0             8            236
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 100  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      3    3
  EDN1 WILD-TYPE  100   65
     clus
vv    EDN1 MUTATED EDN1 WILD-TYPE
  NO             3            100
  YES            3             65
[1] 2 2
[1] FALSE
D95V10, binary
                cls
clus               0   1
  EDN1 MUTATED     1   8
  EDN1 WILD-TYPE  35 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      1    8
  EDN1 WILD-TYPE   35  231
     clus
vv    EDN1 MUTATED EDN1 WILD-TYPE
  NO             1             35
  YES            8            231
[1] 2 2
[1] FALSE
D95V11, continuous
D95V12, binary
                cls
clus               0   1
  EDN1 MUTATED     1   8
  EDN1 WILD-TYPE 105 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      1    8
  EDN1 WILD-TYPE  105  162
        clus
vv       EDN1 MUTATED EDN1 WILD-TYPE
  FEMALE            1            105
  MALE              8            162
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EDN1 MUTATED       0                         0     9
  EDN1 WILD-TYPE     3                         1   263
D95V13, multiclass
                           clus
vv                          EDN1 MUTATED EDN1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                9            263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V14, binary
                cls
clus               0   1
  EDN1 MUTATED     0   9
  EDN1 WILD-TYPE   3 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDN1 MUTATED      0    9
  EDN1 WILD-TYPE    3  260
                        clus
vv                       EDN1 MUTATED EDN1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            9            260
[1] 2 2
[1] FALSE

Clustering(96) Variable = HTR7 MUTATION ANALYSIS
D96V1, survival
                sevent
clus2              0   1
  HTR7 MUTATED     3   6
  HTR7 WILD-TYPE 123 134
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            257 
  HTR7 MUTATED HTR7 WILD-TYPE 
             6            134 
$`HTR7 MUTATED`
TCGA-D3-A2J9 TCGA-DA-A1HV TCGA-EE-A29E TCGA-EE-A29Q TCGA-EE-A2GS TCGA-EE-A3AH 
       21.14        48.79        62.79         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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       14.20        10.78         5.98         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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  HTR7 MUTATED HTR7 WILD-TYPE 
          6.41           0.13 
  HTR7 MUTATED HTR7 WILD-TYPE 
         62.79         125.65 
  HTR7 MUTATED HTR7 WILD-TYPE 
         12.72          17.56 
[1] "6.4 - 62.8 (12.7)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.6"
D96V2, survival
                sevent
clus2              0   1
  HTR7 MUTATED     3   6
  HTR7 WILD-TYPE 126 135
  HTR7 MUTATED HTR7 WILD-TYPE 
             9            261 
  HTR7 MUTATED HTR7 WILD-TYPE 
             6            135 
$`HTR7 MUTATED`
TCGA-D3-A2J9 TCGA-DA-A1HV TCGA-EE-A29E TCGA-EE-A29Q TCGA-EE-A2GS TCGA-EE-A3AH 
       23.77        48.89        63.78        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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        2.60        56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       51.62         3.68        54.51        13.81        23.47       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  HTR7 MUTATED HTR7 WILD-TYPE 
         10.13           0.16 
  HTR7 MUTATED HTR7 WILD-TYPE 
        138.81         357.37 
  HTR7 MUTATED HTR7 WILD-TYPE 
         48.89          53.16 
[1] "10.1 - 138.8 (48.9)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1.8"
D96V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  HTR7 MUTATED                    1             0
  HTR7 WILD-TYPE                 38             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  HTR7 MUTATED                                           4                   4
  HTR7 WILD-TYPE                                        56                 167
D96V4, multiclass
                                           clus
vv                                          HTR7 MUTATED HTR7 WILD-TYPE
  DISTANT METASTASIS                                   1             38
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             56
  REGIONAL LYMPH NODE                                  4            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
  HTR7 MUTATED             0       0       0        0        1        1
  HTR7 WILD-TYPE          10       6      24       10       23       15
                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        32         13         20
                vv
clus             STAGE IIIC STAGE IV
  HTR7 MUTATED            1        0
  HTR7 WILD-TYPE         45       16
D96V5, multiclass
             clus
vv            HTR7 MUTATED HTR7 WILD-TYPE
  I OR II NOS            0             10
  STAGE 0                0              6
  STAGE I                0             24
  STAGE IA               0             10
  STAGE IB               1             23
  STAGE II               1             15
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              0             32
  STAGE IIIA             0             13
  STAGE IIIB             3             20
  STAGE IIIC             1             45
  STAGE IV               0             16
[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    51 58 50 55
D96V6, multiclass
       clus
vv      HTR7 MUTATED HTR7 WILD-TYPE
  T0+T1            1             51
  T2               1             58
  T3               4             50
  T4               2             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
  HTR7 MUTATED     4   1   2   1
  HTR7 WILD-TYPE 135  47  31  35
D96V7, multiclass
    clus
vv   HTR7 MUTATED HTR7 WILD-TYPE
  N0            4            135
  N1            1             47
  N2            2             31
  N3            1             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  HTR7 MUTATED     8   0   0   0   0
  HTR7 WILD-TYPE 236   4   3   2   8
D96V8, multiclass
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  M0             8            236
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 99 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      4    3
  HTR7 WILD-TYPE   99   65
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  NO             4             99
  YES            3             65
[1] 2 2
[1] FALSE
D96V10, binary
                cls
clus               0   1
  HTR7 MUTATED     2   7
  HTR7 WILD-TYPE  34 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      2    7
  HTR7 WILD-TYPE   34  232
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  NO             2             34
  YES            7            232
[1] 2 2
[1] FALSE
D96V11, continuous
D96V12, binary
                cls
clus               0   1
  HTR7 MUTATED     5   4
  HTR7 WILD-TYPE 101 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      5    4
  HTR7 WILD-TYPE  101  166
        clus
vv       HTR7 MUTATED HTR7 WILD-TYPE
  FEMALE            5            101
  MALE              4            166
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HTR7 MUTATED       0                         0     9
  HTR7 WILD-TYPE     3                         1   263
D96V13, multiclass
                           clus
vv                          HTR7 MUTATED HTR7 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                9            263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V14, binary
                cls
clus               0   1
  HTR7 MUTATED     0   9
  HTR7 WILD-TYPE   3 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      0    9
  HTR7 WILD-TYPE    3  260
                        clus
vv                       HTR7 MUTATED HTR7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            9            260
[1] 2 2
[1] FALSE

Clustering(97) Variable = TLR9 MUTATION ANALYSIS
D97V1, survival
                sevent
clus2              0   1
  TLR9 MUTATED    11   7
  TLR9 WILD-TYPE 115 133
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            248 
  TLR9 MUTATED TLR9 WILD-TYPE 
             7            133 
$`TLR9 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A51J TCGA-D9-A3Z1 
       44.19        92.42        46.98         6.31        54.31         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        60.49       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        86.76        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        59.57 
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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       54.74        31.30        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 
       52.01        47.87        13.68        17.72        23.11        21.93 
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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67         5.56       124.31        51.62         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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        33.60        31.40        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       18.41        85.74        15.72        64.47         3.45        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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  TLR9 MUTATED TLR9 WILD-TYPE 
          0.99           0.13 
  TLR9 MUTATED TLR9 WILD-TYPE 
        122.73         125.65 
  TLR9 MUTATED TLR9 WILD-TYPE 
         36.74          16.19 
[1] "1.0 - 122.7 (36.7)" "0.1 - 125.7 (16.2)"
[1] "hr=" "1.7"
D97V2, survival
                sevent
clus2              0   1
  TLR9 MUTATED    11   7
  TLR9 WILD-TYPE 118 134
  TLR9 MUTATED TLR9 WILD-TYPE 
            18            252 
  TLR9 MUTATED TLR9 WILD-TYPE 
             7            134 
$`TLR9 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A51J TCGA-D9-A3Z1 
       62.07       171.58        46.98        13.87       145.12        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       134.40       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        86.76        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        59.57 
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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        2.60        56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       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       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.72       216.92        48.59       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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  TLR9 MUTATED TLR9 WILD-TYPE 
         11.34           0.16 
  TLR9 MUTATED TLR9 WILD-TYPE 
        228.59         357.37 
  TLR9 MUTATED TLR9 WILD-TYPE 
         64.16          51.12 
[1] "11.3 - 228.6 (64.2)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "1.6"
D97V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TLR9 MUTATED                    2             1
  TLR9 WILD-TYPE                 37             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TLR9 MUTATED                                           3                  12
  TLR9 WILD-TYPE                                        57                 159
D97V4, multiclass
                                           clus
vv                                          TLR9 MUTATED TLR9 WILD-TYPE
  DISTANT METASTASIS                                   2             37
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             57
  REGIONAL LYMPH NODE                                 12            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
  TLR9 MUTATED             1       0       2        1        0        0
  TLR9 WILD-TYPE           9       6      22        9       24       16
                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        27         11         23
                vv
clus             STAGE IIIC STAGE IV
  TLR9 MUTATED            3        1
  TLR9 WILD-TYPE         43       15
D97V5, multiclass
             clus
vv            TLR9 MUTATED TLR9 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                2             22
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               0             16
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              5             27
  STAGE IIIA             2             11
  STAGE IIIB             0             23
  STAGE IIIC             3             43
  STAGE IV               1             15
[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    47 56 49 55
D97V6, multiclass
       clus
vv      TLR9 MUTATED TLR9 WILD-TYPE
  T0+T1            5             47
  T2               3             56
  T3               5             49
  T4               2             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
  TLR9 MUTATED     8   4   3   3
  TLR9 WILD-TYPE 131  44  30  33
D97V7, multiclass
    clus
vv   TLR9 MUTATED TLR9 WILD-TYPE
  N0            8            131
  N1            4             44
  N2            3             30
  N3            3             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
  TLR9 MUTATED    17   0   1   0   0
  TLR9 WILD-TYPE 227   4   2   2   8
D97V8, multiclass
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  M0            17            227
  M1             0              4
  M1A            1              2
  M1B            0              2
  M1C            0              8
[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 96 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      7    3
  TLR9 WILD-TYPE   96   65
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  NO             7             96
  YES            3             65
[1] 2 2
[1] FALSE
D97V10, binary
                cls
clus               0   1
  TLR9 MUTATED     4  14
  TLR9 WILD-TYPE  32 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      4   14
  TLR9 WILD-TYPE   32  225
     clus
vv    TLR9 MUTATED TLR9 WILD-TYPE
  NO             4             32
  YES           14            225
[1] 2 2
[1] FALSE
D97V11, continuous
D97V12, binary
                cls
clus               0   1
  TLR9 MUTATED     5  13
  TLR9 WILD-TYPE 101 157
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      5   13
  TLR9 WILD-TYPE  101  157
        clus
vv       TLR9 MUTATED TLR9 WILD-TYPE
  FEMALE            5            101
  MALE             13            157
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TLR9 MUTATED       0                         0    18
  TLR9 WILD-TYPE     3                         1   254
D97V13, multiclass
                           clus
vv                          TLR9 MUTATED TLR9 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               18            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"
D97V14, binary
                cls
clus               0   1
  TLR9 MUTATED     0  18
  TLR9 WILD-TYPE   3 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR9 MUTATED      0   18
  TLR9 WILD-TYPE    3  251
                        clus
vv                       TLR9 MUTATED TLR9 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           18            251
[1] 2 2
[1] FALSE

Clustering(98) Variable = MYH1 MUTATION ANALYSIS
D98V1, survival
                sevent
clus2              0   1
  MYH1 MUTATED    37  29
  MYH1 WILD-TYPE  89 111
  MYH1 MUTATED MYH1 WILD-TYPE 
            66            200 
  MYH1 MUTATED MYH1 WILD-TYPE 
            29            111 
$`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        44.19        64.44        82.29 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A6EA TCGA-D9-A6EC 
       54.31        32.61        13.68        17.72        11.31        13.22 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C 
       35.80        36.69        13.35        11.57        12.20         4.34 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        9.21         7.99        11.15        62.79        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GR 
       39.62        36.30        34.29        47.21        19.43         1.15 
TCGA-EE-A2GT TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       34.98         9.53         2.73        63.42       111.91        56.02 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AG 
       60.49        53.16        52.67         5.56         3.68        15.95 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       12.72        21.60        21.60         0.95        27.35        18.41 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19P TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-FR-A44A 
       31.40        18.61        34.68        78.44        11.74        85.74 
TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TU 
        7.30        47.38        52.08         5.23         0.99         0.13 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-QB-A6FS TCGA-RP-A693 
        0.85        11.61        84.72        10.13         5.79         0.33 

$`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        86.76        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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       32.28        21.44        25.78        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        21.93         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        23.15        19.00        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 
       60.23        15.85         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 
       32.15         8.09        11.31        49.22         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       51.12        17.98        60.00        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        55.69         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       125.65        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        51.62        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        21.73        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-A19T 
       13.45        28.60        42.84         9.57        36.07         6.58 
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-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-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-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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         2.27         0.20         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        7.23        44.28        31.33        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-RP-A694 
       14.70         0.69 

  MYH1 MUTATED MYH1 WILD-TYPE 
          0.13           0.16 
  MYH1 MUTATED MYH1 WILD-TYPE 
        111.91         125.65 
  MYH1 MUTATED MYH1 WILD-TYPE 
        20.515         15.930 
[1] "0.1 - 111.9 (20.5)" "0.2 - 125.7 (15.9)"
[1] "hr=" "1.4"
D98V2, survival
                sevent
clus2              0   1
  MYH1 MUTATED    37  30
  MYH1 WILD-TYPE  92 111
  MYH1 MUTATED MYH1 WILD-TYPE 
            67            203 
  MYH1 MUTATED MYH1 WILD-TYPE 
            30            111 
$`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        62.07        66.08       166.52 
TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1JX TCGA-D9-A6EA 
      145.12        63.81       178.32        18.18         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        17.29        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        63.78        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ 
        2.60        56.84        36.82        67.43       208.04        89.33 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2ML 
       14.30        44.88        47.28       268.73        96.23       203.05 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AD 
      167.90       134.40       162.48        71.21        53.26         3.68 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD 
       23.47       138.81        36.95        64.08       201.80        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19P TCGA-ER-A1A1 TCGA-ER-A2NH 
       51.35        31.40        35.44       162.08        79.99        32.05 
TCGA-FR-A44A TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3R5 
      174.21        27.72       101.26        74.73        27.02        22.92 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-QB-A6FS 
       47.54         2.04        11.74        84.72        10.13         6.67 
TCGA-RP-A693 
        0.33 

$`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        86.76        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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       32.94        22.62        26.89       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       54.02        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       133.81        91.56        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       195.02        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        86.14        59.28       314.56       161.03 
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       126.81 
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 
      158.63        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 
       51.62        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       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25         8.88       148.18        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21         6.77        92.98        15.72       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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        23.93       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-GN-A262 TCGA-GN-A264 
        0.16        19.30         9.90         7.23       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A694 
       64.44        62.79        32.48        39.58         0.69 

  MYH1 MUTATED MYH1 WILD-TYPE 
          0.33           0.16 
  MYH1 MUTATED MYH1 WILD-TYPE 
        268.73         357.37 
  MYH1 MUTATED MYH1 WILD-TYPE 
         61.18          50.76 
[1] "0.3 - 268.7 (61.2)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1.3"
D98V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  MYH1 MUTATED                    9             2
  MYH1 WILD-TYPE                 30             3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  MYH1 MUTATED                                          13                  43
  MYH1 WILD-TYPE                                        47                 128
D98V4, multiclass
                                           clus
vv                                          MYH1 MUTATED MYH1 WILD-TYPE
  DISTANT METASTASIS                                   9             30
  PRIMARY TUMOR                                        2              3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           13             47
  REGIONAL LYMPH NODE                                 43            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       6        5        3        7
  MYH1 WILD-TYPE           9       4      18        5       21        9
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MYH1 MUTATED           2         4         0        12          2          6
  MYH1 WILD-TYPE         8        10         9        20         11         17
                vv
clus             STAGE IIIC STAGE IV
  MYH1 MUTATED            8        3
  MYH1 WILD-TYPE         38       13
D98V5, multiclass
             clus
vv            MYH1 MUTATED MYH1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                2              4
  STAGE I                6             18
  STAGE IA               5              5
  STAGE IB               3             21
  STAGE II               7              9
  STAGE IIA              2              8
  STAGE IIB              4             10
  STAGE IIC              0              9
  STAGE III             12             20
  STAGE IIIA             2             11
  STAGE IIIB             6             17
  STAGE IIIC             8             38
  STAGE IV               3             13
[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 11 18  9
  MYH1 WILD-TYPE    38 48 36 48
D98V6, multiclass
       clus
vv      MYH1 MUTATED MYH1 WILD-TYPE
  T0+T1           14             38
  T2              11             48
  T3              18             36
  T4               9             48
[1] 4 2
[1] TRUE
[1] "dimension of 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    32  15   6   7
  MYH1 WILD-TYPE 107  33  27  29
D98V7, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  N0           32            107
  N1           15             33
  N2            6             27
  N3            7             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
  MYH1 MUTATED    60   0   0   1   2
  MYH1 WILD-TYPE 184   4   3   1   6
D98V8, multiclass
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  M0            60            184
  M1             0              4
  M1A            0              3
  M1B            1              1
  M1C            2              6
[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 77 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     26   11
  MYH1 WILD-TYPE   77   57
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  NO            26             77
  YES           11             57
[1] 2 2
[1] FALSE
D98V10, binary
                cls
clus               0   1
  MYH1 MUTATED    12  55
  MYH1 WILD-TYPE  24 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     12   55
  MYH1 WILD-TYPE   24  184
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  NO            12             24
  YES           55            184
[1] 2 2
[1] FALSE
D98V11, continuous
D98V12, binary
                cls
clus               0   1
  MYH1 MUTATED    16  51
  MYH1 WILD-TYPE  90 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     16   51
  MYH1 WILD-TYPE   90  119
        clus
vv       MYH1 MUTATED MYH1 WILD-TYPE
  FEMALE           16             90
  MALE             51            119
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYH1 MUTATED       0                         0    67
  MYH1 WILD-TYPE     3                         1   205
D98V13, multiclass
                           clus
vv                          MYH1 MUTATED MYH1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               67            205
[1] 3 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  64
  MYH1 WILD-TYPE   2 205
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED      1   64
  MYH1 WILD-TYPE    2  205
                        clus
vv                       MYH1 MUTATED MYH1 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           64            205
[1] 2 2
[1] FALSE

Clustering(99) Variable = EPHA3 MUTATION ANALYSIS
D99V1, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    17  13
  EPHA3 WILD-TYPE 109 127
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             30             236 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             13             127 
$`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        25.78        17.72 
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        15.85 
TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 
       39.62         9.67        30.08        28.31        55.69        98.27 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A199 TCGA-FS-A1Z3 
       47.51        63.42        60.49        27.35         5.72        14.24 
TCGA-FS-A1ZK TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-GN-A266 TCGA-RP-A694 
       12.89         0.99         0.13        11.61        10.13         0.69 

$`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        86.76        44.19         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        59.57       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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87        13.68        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        13.22 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 
       10.55         6.31         8.12         1.12         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       60.23         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        62.79         8.55        36.85         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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       32.15         8.09        11.31        49.22        36.30        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       51.12        34.29        17.98        60.00        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        33.83         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       34.98        36.33         8.84         2.70         6.18         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
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        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22         0.95        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        33.60        31.40        18.61        12.95        38.40 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       19.53        11.08         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 
        5.79         0.33 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
           0.13            0.16 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
          98.27          125.65 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         16.785          16.900 
[1] "0.1 - 98.3 (16.8)"  "0.2 - 125.7 (16.9)"
[1] "hr=" "1.3"
D99V2, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    17  13
  EPHA3 WILD-TYPE 112 128
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             30             240 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             13             128 
$`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        26.89        18.18 
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        91.56 
TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M6 
       56.84        39.29        48.72        75.48       126.81       129.27 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A199 TCGA-FS-A1Z3 
       61.51        96.23       134.40        27.35         9.17        20.91 
TCGA-FS-A1ZK TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C9 TCGA-GN-A266 TCGA-RP-A694 
       23.93        22.92        47.54        11.74        10.13         0.69 

$`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        86.76        62.07       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        59.57       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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       178.32       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        22.29         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 
       68.25        54.02        17.29        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       133.81       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 
       63.78        72.07        64.64         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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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-A2MF 
       21.67        28.83        19.76        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       158.63       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       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        35.44        13.94        50.76        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45        77.88         0.20         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
           0.69            0.16 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         134.40          357.37 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         43.135          53.225 
[1] "0.7 - 134.4 (43.1)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.2"
D99V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  EPHA3 MUTATED                    6             1
  EPHA3 WILD-TYPE                 33             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  EPHA3 MUTATED                                           7                  16
  EPHA3 WILD-TYPE                                        53                 155
D99V4, multiclass
                                           clus
vv                                          EPHA3 MUTATED EPHA3 WILD-TYPE
  DISTANT METASTASIS                                    6              33
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             7              53
  REGIONAL LYMPH NODE                                  16             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
  EPHA3 MUTATED             0       1       4        2        2        2
  EPHA3 WILD-TYPE          10       5      20        8       22       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  EPHA3 MUTATED           0         0         1         5          2          2
  EPHA3 WILD-TYPE        10        14         8        27         11         21
                 vv
clus              STAGE IIIC STAGE IV
  EPHA3 MUTATED            4        3
  EPHA3 WILD-TYPE         42       13
D99V5, multiclass
             clus
vv            EPHA3 MUTATED EPHA3 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 4              20
  STAGE IA                2               8
  STAGE IB                2              22
  STAGE II                2              14
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               5              27
  STAGE IIIA              2              11
  STAGE IIIB              2              21
  STAGE IIIC              4              42
  STAGE IV                3              13
[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    45 54 52 49
D99V6, multiclass
       clus
vv      EPHA3 MUTATED EPHA3 WILD-TYPE
  T0+T1             7              45
  T2                5              54
  T3                2              52
  T4                8              49
[1] 4 2
[1] TRUE
[1] "dimension of 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 125  40  30  35
D99V7, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  N0            14             125
  N1             8              40
  N2             3              30
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  EPHA3 MUTATED    24   1   0   0   2
  EPHA3 WILD-TYPE 220   3   3   2   6
D99V8, multiclass
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  M0             24             220
  M1              1               3
  M1A             0               3
  M1B             0               2
  M1C             2               6
[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 91 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     12    5
  EPHA3 WILD-TYPE   91   63
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO             12              91
  YES             5              63
[1] 2 2
[1] FALSE
D99V10, binary
                 cls
clus                0   1
  EPHA3 MUTATED     7  23
  EPHA3 WILD-TYPE  29 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      7   23
  EPHA3 WILD-TYPE   29  216
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO              7              29
  YES            23             216
[1] 2 2
[1] FALSE
D99V11, continuous
D99V12, binary
                 cls
clus                0   1
  EPHA3 MUTATED    10  20
  EPHA3 WILD-TYPE  96 150
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     10   20
  EPHA3 WILD-TYPE   96  150
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  FEMALE            10              96
  MALE              20             150
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHA3 MUTATED       0                         0    30
  EPHA3 WILD-TYPE     3                         1   242
D99V13, multiclass
                           clus
vv                          EPHA3 MUTATED EPHA3 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                30             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"
D99V14, binary
                 cls
clus                0   1
  EPHA3 MUTATED     0  29
  EPHA3 WILD-TYPE   3 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      0   29
  EPHA3 WILD-TYPE    3  240
                        clus
vv                       EPHA3 MUTATED EPHA3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            29             240
[1] 2 2
[1] FALSE

Clustering(100) Variable = ARL16 MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2               0   1
  ARL16 MUTATED     4   3
  ARL16 WILD-TYPE 122 137
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             259 
  ARL16 MUTATED ARL16 WILD-TYPE 
              3             137 
$`ARL16 MUTATED`
TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2GU TCGA-EE-A2MS TCGA-EE-A3JD TCGA-ER-A2NC 
       44.19         7.99        36.33        53.16        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        86.76        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       15.85         9.21         1.18         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69 
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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        60.49        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZU 
       47.38        52.08         8.65         8.81        49.15         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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  ARL16 MUTATED ARL16 WILD-TYPE 
           7.99            0.13 
  ARL16 MUTATED ARL16 WILD-TYPE 
          53.16          125.65 
  ARL16 MUTATED ARL16 WILD-TYPE 
          36.33           16.24 
[1] "8.0 - 53.2 (36.3)"  "0.1 - 125.7 (16.2)"
[1] "hr=" "1.5"
D100V2, survival
                 sevent
clus2               0   1
  ARL16 MUTATED     4   3
  ARL16 WILD-TYPE 125 138
  ARL16 MUTATED ARL16 WILD-TYPE 
              7             263 
  ARL16 MUTATED ARL16 WILD-TYPE 
              3             138 
$`ARL16 MUTATED`
TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2GU TCGA-EE-A2MS TCGA-EE-A3JD TCGA-ER-A2NC 
       62.07        63.35        94.82       162.48        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        86.76        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       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       134.40        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19       201.80        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  ARL16 MUTATED ARL16 WILD-TYPE 
          27.35            0.16 
  ARL16 MUTATED ARL16 WILD-TYPE 
         162.48          357.37 
  ARL16 MUTATED ARL16 WILD-TYPE 
          62.07           51.35 
[1] "27.4 - 162.5 (62.1)" "0.2 - 357.4 (51.4)" 
[1] "hr=" "1.3"
D100V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ARL16 MUTATED                    4             0
  ARL16 WILD-TYPE                 35             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ARL16 MUTATED                                           0                   3
  ARL16 WILD-TYPE                                        60                 168
D100V4, multiclass
                                           clus
vv                                          ARL16 MUTATED ARL16 WILD-TYPE
  DISTANT METASTASIS                                    4              35
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             0              60
  REGIONAL LYMPH NODE                                   3             168
[1] 4 2
[1] 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      24        8       23       15
                 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        30         12         23
                 vv
clus              STAGE IIIC STAGE IV
  ARL16 MUTATED            0        0
  ARL16 WILD-TYPE         46       16
D100V5, multiclass
             clus
vv            ARL16 MUTATED ARL16 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                2               8
  STAGE IB                1              23
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              1              12
  STAGE IIIB              0              23
  STAGE IIIC              0              46
  STAGE IV                0              16
[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    50 57 52 57
D100V6, multiclass
       clus
vv      ARL16 MUTATED ARL16 WILD-TYPE
  T0+T1             2              50
  T2                2              57
  T3                2              52
  T4                0              57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ARL16 MUTATED     4   2   1   0
  ARL16 WILD-TYPE 135  46  32  36
D100V7, multiclass
    clus
vv   ARL16 MUTATED ARL16 WILD-TYPE
  N0             4             135
  N1             2              46
  N2             1              32
  N3             0              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               M0  M1 M1A M1B M1C
  ARL16 MUTATED     7   0   0   0   0
  ARL16 WILD-TYPE 237   4   3   2   8
D100V8, multiclass
     clus
vv    ARL16 MUTATED ARL16 WILD-TYPE
  M0              7             237
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 98 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      5    0
  ARL16 WILD-TYPE   98   68
     clus
vv    ARL16 MUTATED ARL16 WILD-TYPE
  NO              5              98
  YES             0              68
[1] 2 2
[1] FALSE
D100V10, binary
                 cls
clus                0   1
  ARL16 MUTATED     1   6
  ARL16 WILD-TYPE  35 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      1    6
  ARL16 WILD-TYPE   35  233
     clus
vv    ARL16 MUTATED ARL16 WILD-TYPE
  NO              1              35
  YES             6             233
[1] 2 2
[1] FALSE
D100V11, continuous
D100V12, binary
                 cls
clus                0   1
  ARL16 MUTATED     1   6
  ARL16 WILD-TYPE 105 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      1    6
  ARL16 WILD-TYPE  105  164
        clus
vv       ARL16 MUTATED ARL16 WILD-TYPE
  FEMALE             1             105
  MALE               6             164
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARL16 MUTATED       0                         0     7
  ARL16 WILD-TYPE     3                         1   265
D100V13, multiclass
                           clus
vv                          ARL16 MUTATED ARL16 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 7             265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V14, binary
                 cls
clus                0   1
  ARL16 MUTATED     0   6
  ARL16 WILD-TYPE   3 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL16 MUTATED      0    6
  ARL16 WILD-TYPE    3  263
                        clus
vv                       ARL16 MUTATED ARL16 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             263
[1] 2 2
[1] FALSE

Clustering(101) Variable = DDX17 MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     5   6
  DDX17 WILD-TYPE 121 134
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             255 
  DDX17 MUTATED DDX17 WILD-TYPE 
              6             134 
$`DDX17 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A5GR TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2MD 
        8.52        13.68         9.99        36.30        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        86.76        11.41        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         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        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        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        55.69         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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        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       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  DDX17 MUTATED DDX17 WILD-TYPE 
           0.99            0.13 
  DDX17 MUTATED DDX17 WILD-TYPE 
         122.73          125.65 
  DDX17 MUTATED DDX17 WILD-TYPE 
          11.11           17.56 
[1] "1.0 - 122.7 (11.1)" "0.1 - 125.7 (17.6)"
[1] "hr=" "1.2"
D101V2, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     5   6
  DDX17 WILD-TYPE 124 135
  DDX17 MUTATED DDX17 WILD-TYPE 
             11             259 
  DDX17 MUTATED DDX17 WILD-TYPE 
              6             135 
$`DDX17 MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A5GR TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2MD 
       16.67       178.32        35.93        36.82        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        86.76        11.87        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        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        86.14        59.28        67.43       314.56       161.03 
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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21        53.26       124.31        51.62         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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58       148.08        31.40        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  DDX17 MUTATED DDX17 WILD-TYPE 
          16.67            0.16 
  DDX17 MUTATED DDX17 WILD-TYPE 
         178.32          357.37 
  DDX17 MUTATED DDX17 WILD-TYPE 
          35.93           53.26 
[1] "16.7 - 178.3 (35.9)" "0.2 - 357.4 (53.3)" 
[1] "hr=" "1.3"
D101V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DDX17 MUTATED                    1             0
  DDX17 WILD-TYPE                 38             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DDX17 MUTATED                                           1                   9
  DDX17 WILD-TYPE                                        59                 162
D101V4, multiclass
                                           clus
vv                                          DDX17 MUTATED DDX17 WILD-TYPE
  DISTANT METASTASIS                                    1              38
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                   9             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
  DDX17 MUTATED             0       0       0        1        0        1
  DDX17 WILD-TYPE          10       6      24        9       24       15
                 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        29         13         22
                 vv
clus              STAGE IIIC STAGE IV
  DDX17 MUTATED            2        0
  DDX17 WILD-TYPE         44       16
D101V5, multiclass
             clus
vv            DDX17 MUTATED DDX17 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                1               9
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               3              29
  STAGE IIIA              0              13
  STAGE IIIB              1              22
  STAGE IIIC              2              44
  STAGE IV                0              16
[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    49 59 52 54
D101V6, multiclass
       clus
vv      DDX17 MUTATED DDX17 WILD-TYPE
  T0+T1             3              49
  T2                0              59
  T3                2              52
  T4                3              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
  DDX17 MUTATED     5   2   4   0
  DDX17 WILD-TYPE 134  46  29  36
D101V7, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             5             134
  N1             2              46
  N2             4              29
  N3             0              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               M0  M1 M1A M1B M1C
  DDX17 MUTATED    11   0   0   0   0
  DDX17 WILD-TYPE 233   4   3   2   8
D101V8, multiclass
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  M0             11             233
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 102  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      1    5
  DDX17 WILD-TYPE  102   63
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              1             102
  YES             5              63
[1] 2 2
[1] FALSE
D101V10, binary
                 cls
clus                0   1
  DDX17 MUTATED     1  10
  DDX17 WILD-TYPE  35 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      1   10
  DDX17 WILD-TYPE   35  229
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              1              35
  YES            10             229
[1] 2 2
[1] FALSE
D101V11, continuous
D101V12, binary
                 cls
clus                0   1
  DDX17 MUTATED     2   9
  DDX17 WILD-TYPE 104 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      2    9
  DDX17 WILD-TYPE  104  161
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             2             104
  MALE               9             161
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX17 MUTATED       0                         0    11
  DDX17 WILD-TYPE     3                         1   261
D101V13, multiclass
                           clus
vv                          DDX17 MUTATED DDX17 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             261
[1] 3 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   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      0   11
  DDX17 WILD-TYPE    3  258
                        clus
vv                       DDX17 MUTATED DDX17 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             258
[1] 2 2
[1] FALSE

Clustering(102) Variable = MAN1A1 MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  MAN1A1 MUTATED     6   8
  MAN1A1 WILD-TYPE 120 132
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              14              252 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
               8              132 
$`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        62.79         9.50        60.49 
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 
TCGA-GF-A6C9 TCGA-RP-A694 
       11.61         0.69 

$`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        86.76        11.41        44.19 
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 
       59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         1.08        39.62        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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       12.72         3.22        21.60        16.14        22.22         0.95 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         0.85        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 

  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
            0.69             0.13 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
           62.79           125.65 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
          15.995           16.900 
[1] "0.7 - 62.8 (16.0)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.3"
D102V2, survival
                  sevent
clus2                0   1
  MAN1A1 MUTATED     6   8
  MAN1A1 WILD-TYPE 123 133
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              14              256 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
               8              133 
$`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        63.78        18.61       134.40 
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 
TCGA-GF-A6C9 TCGA-RP-A694 
       11.74         0.69 

$`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        86.76        11.87        62.07 
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 
       59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       56.84        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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      148.08        31.40        35.44        13.94        50.76        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85        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        19.30         9.90         7.23         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       32.48        39.58         6.67         0.33 

  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
            0.69             0.16 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
          357.37           314.56 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
          32.150           53.175 
[1] "0.7 - 357.4 (32.2)" "0.2 - 314.6 (53.2)"
[1] "hr=" "1"  
D102V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MAN1A1 MUTATED                    3             0
  MAN1A1 WILD-TYPE                 36             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MAN1A1 MUTATED                                           2
  MAN1A1 WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  MAN1A1 MUTATED                     9
  MAN1A1 WILD-TYPE                 162
D102V4, multiclass
                                           clus
vv                                          MAN1A1 MUTATED MAN1A1 WILD-TYPE
  DISTANT METASTASIS                                     3               36
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                    9              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
  MAN1A1 MUTATED             2       0       1        0        1        1
  MAN1A1 WILD-TYPE           8       6      23       10       23       15
                  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        28         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAN1A1 MUTATED            2          1        1
  MAN1A1 WILD-TYPE         21         45       15
D102V5, multiclass
             clus
vv            MAN1A1 MUTATED MAN1A1 WILD-TYPE
  I OR II NOS              2                8
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 1               15
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                4               28
  STAGE IIIA               1               12
  STAGE IIIB               2               21
  STAGE IIIC               1               45
  STAGE IV                 1               15
[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    51 57 51 55
D102V6, multiclass
       clus
vv      MAN1A1 MUTATED MAN1A1 WILD-TYPE
  T0+T1              1               51
  T2                 2               57
  T3                 3               51
  T4                 2               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
  MAN1A1 MUTATED     5   3   3   1
  MAN1A1 WILD-TYPE 134  45  30  35
D102V7, multiclass
    clus
vv   MAN1A1 MUTATED MAN1A1 WILD-TYPE
  N0              5              134
  N1              3               45
  N2              3               30
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  MAN1A1 MUTATED    12   0   0   0   1
  MAN1A1 WILD-TYPE 232   4   3   2   7
D102V8, multiclass
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  M0              12              232
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 98 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      5    2
  MAN1A1 WILD-TYPE   98   66
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  NO               5               98
  YES              2               66
[1] 2 2
[1] FALSE
D102V10, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     4  10
  MAN1A1 WILD-TYPE  32 229
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      4   10
  MAN1A1 WILD-TYPE   32  229
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  NO               4               32
  YES             10              229
[1] 2 2
[1] FALSE
D102V11, continuous
D102V12, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     2  12
  MAN1A1 WILD-TYPE 104 158
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      2   12
  MAN1A1 WILD-TYPE  104  158
        clus
vv       MAN1A1 MUTATED MAN1A1 WILD-TYPE
  FEMALE              2              104
  MALE               12              158
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAN1A1 MUTATED       0                         0    14
  MAN1A1 WILD-TYPE     3                         1   258
D102V13, multiclass
                           clus
vv                          MAN1A1 MUTATED MAN1A1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 14              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"
D102V14, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     0  14
  MAN1A1 WILD-TYPE   3 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      0   14
  MAN1A1 WILD-TYPE    3  255
                        clus
vv                       MAN1A1 MUTATED MAN1A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             14              255
[1] 2 2
[1] FALSE

Clustering(103) Variable = ADAM30 MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED    10  18
  ADAM30 WILD-TYPE 116 122
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              28              238 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              18              122 
$`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        62.79         8.09        30.08 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3JA 
        9.53         2.73        60.49        52.67       124.31        22.22 
TCGA-EE-A3JD TCGA-ER-A19E TCGA-ER-A19P TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
       27.35        11.90        34.68        12.89         8.65         5.23 
TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 
        0.99        11.61        44.28        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 
       86.76        11.41        44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN 
       14.83        13.15        23.15        19.00        13.35        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        60.23         4.34        15.85         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 
       36.85         1.08        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        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        55.69         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       125.65 
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        53.16 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14         0.95        18.41        21.73        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-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       13.45        28.60        42.84         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        12.92        47.38        52.08         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        0.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            0.20             0.13 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          124.31           125.65 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          12.545           17.720 
[1] "0.2 - 124.3 (12.5)" "0.1 - 125.7 (17.7)"
[1] "hr=" "1.3"
D103V2, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED    10  18
  ADAM30 WILD-TYPE 119 123
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              28              242 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              18              123 
$`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        63.78        37.35        48.72 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3JA 
       47.28       268.73       134.40        71.21       124.31        53.19 
TCGA-EE-A3JD TCGA-ER-A19E TCGA-ER-A19P TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
       27.35        13.02       162.08        23.93       133.55        27.02 
TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 
       22.92        11.74       139.89        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 
       86.76        11.87        62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       56.84        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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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       126.81 
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       158.63       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       162.48        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB 
      172.18       127.20        36.95        64.08        34.32       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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-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-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-A264 
        0.16        19.30         9.90         7.23         2.04       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
           10.13             0.16 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          268.73           357.37 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          45.355           53.210 
[1] "10.1 - 268.7 (45.4)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1.4"
D103V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ADAM30 MUTATED                    4             0
  ADAM30 WILD-TYPE                 35             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ADAM30 MUTATED                                           5
  ADAM30 WILD-TYPE                                        55
                  vv
clus               REGIONAL LYMPH NODE
  ADAM30 MUTATED                    19
  ADAM30 WILD-TYPE                 152
D103V4, multiclass
                                           clus
vv                                          ADAM30 MUTATED ADAM30 WILD-TYPE
  DISTANT METASTASIS                                     4               35
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              5               55
  REGIONAL LYMPH NODE                                   19              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       2        1        5        2
  ADAM30 WILD-TYPE           9       5      22        9       19       14
                  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        29         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED            3          3        0
  ADAM30 WILD-TYPE         20         43       16
D103V5, multiclass
             clus
vv            ADAM30 MUTATED ADAM30 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  1                5
  STAGE I                  2               22
  STAGE IA                 1                9
  STAGE IB                 5               19
  STAGE II                 2               14
  STAGE IIA                0               10
  STAGE IIB                3               11
  STAGE IIC                1                8
  STAGE III                3               29
  STAGE IIIA               0               13
  STAGE IIIB               3               20
  STAGE IIIC               3               43
  STAGE IV                 0               16
[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  7  6  2
  ADAM30 WILD-TYPE    49 52 48 55
D103V6, multiclass
       clus
vv      ADAM30 MUTATED ADAM30 WILD-TYPE
  T0+T1              3               49
  T2                 7               52
  T3                 6               48
  T4                 2               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
  ADAM30 MUTATED    17   1   5   2
  ADAM30 WILD-TYPE 122  47  28  34
D103V7, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0             17              122
  N1              1               47
  N2              5               28
  N3              2               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ADAM30 MUTATED    25   0   0   0   0
  ADAM30 WILD-TYPE 219   4   3   2   8
D103V8, multiclass
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  M0              25              219
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 94 61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      9    7
  ADAM30 WILD-TYPE   94   61
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               9               94
  YES              7               61
[1] 2 2
[1] FALSE
D103V10, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     4  24
  ADAM30 WILD-TYPE  32 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      4   24
  ADAM30 WILD-TYPE   32  215
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               4               32
  YES             24              215
[1] 2 2
[1] FALSE
D103V11, continuous
D103V12, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     9  19
  ADAM30 WILD-TYPE  97 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      9   19
  ADAM30 WILD-TYPE   97  151
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE              9               97
  MALE               19              151
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM30 MUTATED       1                         0    27
  ADAM30 WILD-TYPE     2                         1   245
D103V13, multiclass
                           clus
vv                          ADAM30 MUTATED ADAM30 WILD-TYPE
  ASIAN                                  1                2
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 27              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"
D103V14, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     1  27
  ADAM30 WILD-TYPE   2 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      1   27
  ADAM30 WILD-TYPE    2  242
                        clus
vv                       ADAM30 MUTATED ADAM30 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             27              242
[1] 2 2
[1] FALSE

Clustering(104) Variable = NBEAL1 MUTATION ANALYSIS
D104V1, survival
                  sevent
clus2                0   1
  NBEAL1 MUTATED    14  14
  NBEAL1 WILD-TYPE 112 126
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              28              238 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              14              126 
$`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        86.76        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        62.79        34.29        60.00        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        60.49         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 
       44.28        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        44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        1.35         5.13         4.31        60.23         4.34        15.85 
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        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       17.98        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        55.69         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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46         2.73         7.96        14.56       125.65       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        53.16        52.67 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        51.62        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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-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-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       28.60        42.84        34.68        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A4FD 
        7.36        28.73        14.20        10.78         5.98         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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        7.23         0.85        11.61        31.33        16.24        15.42 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
            3.68             0.13 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
          124.31           125.65 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
          24.245           16.355 
[1] "3.7 - 124.3 (24.2)" "0.1 - 125.7 (16.4)"
[1] "hr=" "1.3"
D104V2, survival
                  sevent
clus2                0   1
  NBEAL1 MUTATED    15  14
  NBEAL1 WILD-TYPE 114 127
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              29              241 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
              14              127 
$`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        86.76        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        63.78        67.43       161.03 
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       134.40        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       139.89        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        62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GJ 
       39.29        86.14        59.28       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       126.81        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-A2MF TCGA-EE-A2MH 
       28.83        19.76        61.51       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       43.23       162.48        71.21       122.73        51.62        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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21         6.77       174.21        15.72       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-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
      117.93        64.44        62.79        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
            3.68             0.16 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
          161.03           357.37 
  NBEAL1 MUTATED NBEAL1 WILD-TYPE 
           58.06            50.76 
[1] "3.7 - 161.0 (58.1)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1"  
D104V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  NBEAL1 MUTATED                    0             0
  NBEAL1 WILD-TYPE                 39             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  NBEAL1 MUTATED                                          10
  NBEAL1 WILD-TYPE                                        50
                  vv
clus               REGIONAL LYMPH NODE
  NBEAL1 MUTATED                    20
  NBEAL1 WILD-TYPE                 151
D104V4, multiclass
                                           clus
vv                                          NBEAL1 MUTATED NBEAL1 WILD-TYPE
  DISTANT METASTASIS                                     0               39
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             10               50
  REGIONAL LYMPH NODE                                   20              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
  NBEAL1 MUTATED             0       2       3        2        3        1
  NBEAL1 WILD-TYPE          10       4      21        8       21       15
                  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        25         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  NBEAL1 MUTATED            1          1        0
  NBEAL1 WILD-TYPE         22         45       16
D104V5, multiclass
             clus
vv            NBEAL1 MUTATED NBEAL1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  2                4
  STAGE I                  3               21
  STAGE IA                 2                8
  STAGE IB                 3               21
  STAGE II                 1               15
  STAGE IIA                1                9
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                7               25
  STAGE IIIA               1               12
  STAGE IIIB               1               22
  STAGE IIIC               1               45
  STAGE IV                 0               16
[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    45 53 48 55
D104V6, multiclass
       clus
vv      NBEAL1 MUTATED NBEAL1 WILD-TYPE
  T0+T1              7               45
  T2                 6               53
  T3                 6               48
  T4                 2               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
  NBEAL1 MUTATED    17   6   3   1
  NBEAL1 WILD-TYPE 122  42  30  35
D104V7, multiclass
    clus
vv   NBEAL1 MUTATED NBEAL1 WILD-TYPE
  N0             17              122
  N1              6               42
  N2              3               30
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  NBEAL1 MUTATED    27   0   0   0   0
  NBEAL1 WILD-TYPE 217   4   3   2   8
D104V8, multiclass
     clus
vv    NBEAL1 MUTATED NBEAL1 WILD-TYPE
  M0              27              217
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 90 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED     13    3
  NBEAL1 WILD-TYPE   90   65
     clus
vv    NBEAL1 MUTATED NBEAL1 WILD-TYPE
  NO              13               90
  YES              3               65
[1] 2 2
[1] FALSE
D104V10, binary
                  cls
clus                 0   1
  NBEAL1 MUTATED     7  23
  NBEAL1 WILD-TYPE  29 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED      7   23
  NBEAL1 WILD-TYPE   29  216
     clus
vv    NBEAL1 MUTATED NBEAL1 WILD-TYPE
  NO               7               29
  YES             23              216
[1] 2 2
[1] FALSE
D104V11, continuous
D104V12, binary
                  cls
clus                 0   1
  NBEAL1 MUTATED     9  21
  NBEAL1 WILD-TYPE  97 149
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED      9   21
  NBEAL1 WILD-TYPE   97  149
        clus
vv       NBEAL1 MUTATED NBEAL1 WILD-TYPE
  FEMALE              9               97
  MALE               21              149
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBEAL1 MUTATED       0                         0    30
  NBEAL1 WILD-TYPE     3                         1   242
D104V13, multiclass
                           clus
vv                          NBEAL1 MUTATED NBEAL1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 30              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"
D104V14, binary
                  cls
clus                 0   1
  NBEAL1 MUTATED     0  30
  NBEAL1 WILD-TYPE   3 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBEAL1 MUTATED      0   30
  NBEAL1 WILD-TYPE    3  239
                        clus
vv                       NBEAL1 MUTATED NBEAL1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             30              239
[1] 2 2
[1] FALSE

Clustering(105) Variable = WDR65 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2               0   1
  WDR65 MUTATED    14   6
  WDR65 WILD-TYPE 112 134
  WDR65 MUTATED WDR65 WILD-TYPE 
             20             246 
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             134 
$`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 
       39.62        51.12        17.98        55.69        60.49       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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         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 
       59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11         4.01        21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        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 
       60.23        15.85         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        62.79         8.55        36.85         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-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       36.33        34.29        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        53.16        52.67         5.56 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
        3.22        22.92        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19F 
        5.72        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZM 
       19.53        11.08         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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       14.20         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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  WDR65 MUTATED WDR65 WILD-TYPE 
           1.71            0.13 
  WDR65 MUTATED WDR65 WILD-TYPE 
         124.31          125.65 
  WDR65 MUTATED WDR65 WILD-TYPE 
          30.00           15.98 
[1] "1.7 - 124.3 (30.0)" "0.1 - 125.7 (16.0)"
[1] "hr=" "2.5"
D105V2, survival
                 sevent
clus2               0   1
  WDR65 MUTATED    14   7
  WDR65 WILD-TYPE 115 134
  WDR65 MUTATED WDR65 WILD-TYPE 
             21             249 
  WDR65 MUTATED WDR65 WILD-TYPE 
              7             134 
$`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        56.84        59.28       314.56       126.81       134.40 
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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       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 
       59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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        22.29 
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        68.25        54.02        17.29        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       133.81        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE 
      102.90        36.82        39.29        86.14        67.43       161.03 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        71.21        53.26        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       13.81        23.47       138.81       172.18       127.20        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        35.44        13.94         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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A4FB TCGA-FS-A4FC 
       77.82        66.67        28.73       174.84        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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  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           50.89 
[1] "6.4 - 314.6 (64.1)" "0.2 - 357.4 (50.9)"
[1] "hr=" "2.2"
D105V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  WDR65 MUTATED                    2             1
  WDR65 WILD-TYPE                 37             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  WDR65 MUTATED                                           6                  12
  WDR65 WILD-TYPE                                        54                 159
D105V4, multiclass
                                           clus
vv                                          WDR65 MUTATED WDR65 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             6              54
  REGIONAL LYMPH NODE                                  12             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
  WDR65 MUTATED             2       1       2        0        2        2
  WDR65 WILD-TYPE           8       5      22       10       22       14
                 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        28         12         22
                 vv
clus              STAGE IIIC STAGE IV
  WDR65 MUTATED            2        1
  WDR65 WILD-TYPE         44       15
D105V5, multiclass
             clus
vv            WDR65 MUTATED WDR65 WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 1               5
  STAGE I                 2              22
  STAGE IA                0              10
  STAGE IB                2              22
  STAGE II                2              14
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               4              28
  STAGE IIIA              1              12
  STAGE IIIB              1              22
  STAGE IIIC              2              44
  STAGE IV                1              15
[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    48 53 51 53
D105V6, multiclass
       clus
vv      WDR65 MUTATED WDR65 WILD-TYPE
  T0+T1             4              48
  T2                6              53
  T3                3              51
  T4                4              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
  WDR65 MUTATED    11   4   2   2
  WDR65 WILD-TYPE 128  44  31  34
D105V7, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  N0            11             128
  N1             4              44
  N2             2              31
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  WDR65 MUTATED    20   0   1   0   0
  WDR65 WILD-TYPE 224   4   2   2   8
D105V8, multiclass
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  M0             20             224
  M1              0               4
  M1A             1               2
  M1B             0               2
  M1C             0               8
[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 96 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      7    6
  WDR65 WILD-TYPE   96   62
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  NO              7              96
  YES             6              62
[1] 2 2
[1] FALSE
D105V10, binary
                 cls
clus                0   1
  WDR65 MUTATED     3  18
  WDR65 WILD-TYPE  33 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      3   18
  WDR65 WILD-TYPE   33  221
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  NO              3              33
  YES            18             221
[1] 2 2
[1] FALSE
D105V11, continuous
D105V12, binary
                 cls
clus                0   1
  WDR65 MUTATED     8  13
  WDR65 WILD-TYPE  98 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      8   13
  WDR65 WILD-TYPE   98  157
        clus
vv       WDR65 MUTATED WDR65 WILD-TYPE
  FEMALE             8              98
  MALE              13             157
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR65 MUTATED       0                         0    21
  WDR65 WILD-TYPE     3                         1   251
D105V13, multiclass
                           clus
vv                          WDR65 MUTATED WDR65 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                21             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"
D105V14, binary
                 cls
clus                0   1
  WDR65 MUTATED     0  21
  WDR65 WILD-TYPE   3 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      0   21
  WDR65 WILD-TYPE    3  248
                        clus
vv                       WDR65 MUTATED WDR65 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            21             248
[1] 2 2
[1] FALSE

Clustering(106) Variable = C6ORF165 MUTATION ANALYSIS
D106V1, survival
                    sevent
clus2                  0   1
  C6ORF165 MUTATED     9  10
  C6ORF165 WILD-TYPE 117 130
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                19                247 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                10                130 
$`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-A2MF TCGA-EE-A2MR TCGA-ER-A19F TCGA-ER-A19H 
       30.08        55.69         2.73        60.49        11.11        34.88 
TCGA-FS-A1ZK TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 
       12.89         5.23         0.99         0.16        11.61        10.13 
TCGA-RP-A693 
        0.33 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31        60.23        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        36.33        51.12        17.98        60.00 
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-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       125.65       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        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZM 
       19.53        11.08         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-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-A3TU 
       10.78         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       17.33         9.90         7.23         0.85        44.28        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 
TCGA-RP-A694 
        0.69 

  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
              0.16               0.13 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             60.49             125.65 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             11.15              17.72 
[1] "0.2 - 60.5 (11.2)"  "0.1 - 125.7 (17.7)"
[1] "hr=" "1.4"
D106V2, survival
                    sevent
clus2                  0   1
  C6ORF165 MUTATED     9  10
  C6ORF165 WILD-TYPE 120 131
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                19                251 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                10                131 
$`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-A2MF TCGA-EE-A2MR TCGA-ER-A19F TCGA-ER-A19H 
       48.72       126.81       268.73       134.40        26.37       152.35 
TCGA-FS-A1ZK TCGA-FS-A1ZZ TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 
       23.93        27.02        22.92         0.16        11.74        10.13 
TCGA-RP-A693 
        0.33 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81        91.56       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        63.78        72.07        64.64         2.60        56.84 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       86.14        59.28       314.56       161.03       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       158.63       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       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19G TCGA-ER-A19J 
       98.40        48.89        12.59        13.02       268.93         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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-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-A5DY TCGA-GF-A3OT 
       49.45        77.88         0.20        47.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23         2.04       139.89       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.69 

  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
              0.16               0.20 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
            268.73             357.37 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             29.82              53.16 
[1] "0.2 - 268.7 (29.8)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1"  
D106V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  C6ORF165 MUTATED                    6             0
  C6ORF165 WILD-TYPE                 33             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  C6ORF165 MUTATED                                           3
  C6ORF165 WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  C6ORF165 MUTATED                    10
  C6ORF165 WILD-TYPE                 161
D106V4, multiclass
                                           clus
vv                                          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  DISTANT METASTASIS                                       6                 33
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                3                 57
  REGIONAL LYMPH NODE                                     10                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       2        2        0        2
  C6ORF165 WILD-TYPE          10       5      22        8       24       14
                    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        30         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C6ORF165 MUTATED            1          1        2
  C6ORF165 WILD-TYPE         22         45       14
D106V5, multiclass
             clus
vv            C6ORF165 MUTATED C6ORF165 WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    1                  5
  STAGE I                    2                 22
  STAGE IA                   2                  8
  STAGE IB                   0                 24
  STAGE II                   2                 14
  STAGE IIA                  0                 10
  STAGE IIB                  2                 12
  STAGE IIC                  0                  9
  STAGE III                  2                 30
  STAGE IIIA                 1                 12
  STAGE IIIB                 1                 22
  STAGE IIIC                 1                 45
  STAGE IV                   2                 14
[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  2  5  1
  C6ORF165 WILD-TYPE    48 57 49 56
D106V6, multiclass
       clus
vv      C6ORF165 MUTATED C6ORF165 WILD-TYPE
  T0+T1                4                 48
  T2                   2                 57
  T3                   5                 49
  T4                   1                 56
[1] 4 2
[1] TRUE
[1] "dimension of 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    12   2   2   0
  C6ORF165 WILD-TYPE 127  46  31  36
D106V7, multiclass
    clus
vv   C6ORF165 MUTATED C6ORF165 WILD-TYPE
  N0               12                127
  N1                2                 46
  N2                2                 31
  N3                0                 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                  M0  M1 M1A M1B M1C
  C6ORF165 MUTATED    15   0   0   0   2
  C6ORF165 WILD-TYPE 229   4   3   2   6
D106V8, multiclass
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  M0                15                229
  M1                 0                  4
  M1A                0                  3
  M1B                0                  2
  M1C                2                  6
[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 97 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      6    3
  C6ORF165 WILD-TYPE   97   65
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  NO                 6                 97
  YES                3                 65
[1] 2 2
[1] FALSE
D106V10, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     3  16
  C6ORF165 WILD-TYPE  33 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      3   16
  C6ORF165 WILD-TYPE   33  223
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  NO                 3                 33
  YES               16                223
[1] 2 2
[1] FALSE
D106V11, continuous
D106V12, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     6  13
  C6ORF165 WILD-TYPE 100 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      6   13
  C6ORF165 WILD-TYPE  100  157
        clus
vv       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  FEMALE                6                100
  MALE                 13                157
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C6ORF165 MUTATED       0                         0    19
  C6ORF165 WILD-TYPE     3                         1   253
D106V13, multiclass
                           clus
vv                          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   19                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"
D106V14, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     1  17
  C6ORF165 WILD-TYPE   2 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      1   17
  C6ORF165 WILD-TYPE    2  252
                        clus
vv                       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               17                252
[1] 2 2
[1] FALSE

Clustering(107) Variable = RNF133 MUTATION ANALYSIS
D107V1, survival
                  sevent
clus2                0   1
  RNF133 MUTATED     4   4
  RNF133 WILD-TYPE 122 136
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              258 
  RNF133 MUTATED RNF133 WILD-TYPE 
               4              136 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.85        11.61        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  RNF133 MUTATED RNF133 WILD-TYPE 
            0.99             0.13 
  RNF133 MUTATED RNF133 WILD-TYPE 
          124.31           125.65 
  RNF133 MUTATED RNF133 WILD-TYPE 
          13.845           16.900 
[1] "1.0 - 124.3 (13.8)" "0.1 - 125.7 (16.9)"
[1] "hr=" "1"  
D107V2, survival
                  sevent
clus2                0   1
  RNF133 MUTATED     4   4
  RNF133 WILD-TYPE 125 137
  RNF133 MUTATED RNF133 WILD-TYPE 
               8              262 
  RNF133 MUTATED RNF133 WILD-TYPE 
               4              137 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  RNF133 MUTATED RNF133 WILD-TYPE 
           10.13             0.16 
  RNF133 MUTATED RNF133 WILD-TYPE 
          215.44           357.37 
  RNF133 MUTATED RNF133 WILD-TYPE 
          77.310           51.815 
[1] "10.1 - 215.4 (77.3)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1.2"
D107V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  RNF133 MUTATED                    2             0
  RNF133 WILD-TYPE                 37             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  RNF133 MUTATED                                           1
  RNF133 WILD-TYPE                                        59
                  vv
clus               REGIONAL LYMPH NODE
  RNF133 MUTATED                     5
  RNF133 WILD-TYPE                 166
D107V4, multiclass
                                           clus
vv                                          RNF133 MUTATED RNF133 WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               59
  REGIONAL LYMPH NODE                                    5              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
  RNF133 MUTATED             0       0       1        0        0        1
  RNF133 WILD-TYPE          10       6      23       10       24       15
                  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        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  RNF133 MUTATED            0          2        1
  RNF133 WILD-TYPE         23         44       15
D107V5, multiclass
             clus
vv            RNF133 MUTATED RNF133 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 0               10
  STAGE IB                 0               24
  STAGE II                 1               15
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               0               13
  STAGE IIIB               0               23
  STAGE IIIC               2               44
  STAGE IV                 1               15
[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    49 58 53 56
D107V6, multiclass
       clus
vv      RNF133 MUTATED RNF133 WILD-TYPE
  T0+T1              3               49
  T2                 1               58
  T3                 1               53
  T4                 1               56
[1] 4 2
[1] TRUE
[1] "dimension of 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   1   2   1
  RNF133 WILD-TYPE 136  47  31  35
D107V7, multiclass
    clus
vv   RNF133 MUTATED RNF133 WILD-TYPE
  N0              3              136
  N1              1               47
  N2              2               31
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  RNF133 MUTATED     6   0   0   0   1
  RNF133 WILD-TYPE 238   4   3   2   7
D107V8, multiclass
     clus
vv    RNF133 MUTATED RNF133 WILD-TYPE
  M0               6              238
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 101  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      2    2
  RNF133 WILD-TYPE  101   66
     clus
vv    RNF133 MUTATED RNF133 WILD-TYPE
  NO               2              101
  YES              2               66
[1] 2 2
[1] FALSE
D107V10, binary
                  cls
clus                 0   1
  RNF133 MUTATED     2   6
  RNF133 WILD-TYPE  34 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      2    6
  RNF133 WILD-TYPE   34  233
     clus
vv    RNF133 MUTATED RNF133 WILD-TYPE
  NO               2               34
  YES              6              233
[1] 2 2
[1] FALSE
D107V11, continuous
D107V12, binary
                  cls
clus                 0   1
  RNF133 MUTATED     2   6
  RNF133 WILD-TYPE 104 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      2    6
  RNF133 WILD-TYPE  104  164
        clus
vv       RNF133 MUTATED RNF133 WILD-TYPE
  FEMALE              2              104
  MALE                6              164
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF133 MUTATED       0                         0     8
  RNF133 WILD-TYPE     3                         1   264
D107V13, multiclass
                           clus
vv                          RNF133 MUTATED RNF133 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              264
[1] 3 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   3 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF133 MUTATED      0    8
  RNF133 WILD-TYPE    3  261
                        clus
vv                       RNF133 MUTATED RNF133 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8              261
[1] 2 2
[1] FALSE

Clustering(108) Variable = GTPBP4 MUTATION ANALYSIS
D108V1, survival
                  sevent
clus2                0   1
  GTPBP4 MUTATED     5   3
  GTPBP4 WILD-TYPE 121 137
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              258 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               3              137 
$`GTPBP4 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2A1 TCGA-EE-A3AA TCGA-EE-A3AG 
       88.50        44.19         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        86.76        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        59.57 
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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
            0.99             0.13 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
          124.31           125.65 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
          33.205           16.355 
[1] "1.0 - 124.3 (33.2)" "0.1 - 125.7 (16.4)"
[1] "hr=" "1.9"
D108V2, survival
                  sevent
clus2                0   1
  GTPBP4 MUTATED     5   3
  GTPBP4 WILD-TYPE 124 138
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               8              262 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
               3              138 
$`GTPBP4 MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JF TCGA-EE-A29A TCGA-EE-A2A1 TCGA-EE-A3AA TCGA-EE-A3AG 
      115.53        62.07        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        86.76        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        59.57 
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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        54.51        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
           22.92             0.16 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
          124.31           357.37 
  GTPBP4 MUTATED GTPBP4 WILD-TYPE 
           62.71            51.12 
[1] "22.9 - 124.3 (62.7)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "1.4"
D108V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  GTPBP4 MUTATED                    2             0
  GTPBP4 WILD-TYPE                 37             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  GTPBP4 MUTATED                                           2
  GTPBP4 WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  GTPBP4 MUTATED                     4
  GTPBP4 WILD-TYPE                 167
D108V4, multiclass
                                           clus
vv                                          GTPBP4 MUTATED GTPBP4 WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                    4              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
  GTPBP4 MUTATED             0       0       0        1        2        0
  GTPBP4 WILD-TYPE          10       6      24        9       22       16
                  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        29         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  GTPBP4 MUTATED            0          0        0
  GTPBP4 WILD-TYPE         23         46       16
D108V5, multiclass
             clus
vv            GTPBP4 MUTATED GTPBP4 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               24
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 0               16
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                3               29
  STAGE IIIA               2               11
  STAGE IIIB               0               23
  STAGE IIIC               0               46
  STAGE IV                 0               16
[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    49 56 53 57
D108V6, multiclass
       clus
vv      GTPBP4 MUTATED GTPBP4 WILD-TYPE
  T0+T1              3               49
  T2                 3               56
  T3                 1               53
  T4                 0               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GTPBP4 MUTATED     3   2   3   0
  GTPBP4 WILD-TYPE 136  46  30  36
D108V7, multiclass
    clus
vv   GTPBP4 MUTATED GTPBP4 WILD-TYPE
  N0              3              136
  N1              2               46
  N2              3               30
  N3              0               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                M0  M1 M1A M1B M1C
  GTPBP4 MUTATED     8   0   0   0   0
  GTPBP4 WILD-TYPE 236   4   3   2   8
D108V8, multiclass
     clus
vv    GTPBP4 MUTATED GTPBP4 WILD-TYPE
  M0               8              236
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 98 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      5    0
  GTPBP4 WILD-TYPE   98   68
     clus
vv    GTPBP4 MUTATED GTPBP4 WILD-TYPE
  NO               5               98
  YES              0               68
[1] 2 2
[1] FALSE
D108V10, binary
                  cls
clus                 0   1
  GTPBP4 MUTATED     2   6
  GTPBP4 WILD-TYPE  34 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      2    6
  GTPBP4 WILD-TYPE   34  233
     clus
vv    GTPBP4 MUTATED GTPBP4 WILD-TYPE
  NO               2               34
  YES              6              233
[1] 2 2
[1] FALSE
D108V11, continuous
D108V12, binary
                  cls
clus                 0   1
  GTPBP4 MUTATED     0   8
  GTPBP4 WILD-TYPE 106 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      0    8
  GTPBP4 WILD-TYPE  106  162
        clus
vv       GTPBP4 MUTATED GTPBP4 WILD-TYPE
  FEMALE              0              106
  MALE                8              162
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTPBP4 MUTATED       0                         0     8
  GTPBP4 WILD-TYPE     3                         1   264
D108V13, multiclass
                           clus
vv                          GTPBP4 MUTATED GTPBP4 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              264
[1] 3 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   3 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTPBP4 MUTATED      0    7
  GTPBP4 WILD-TYPE    3  262
                        clus
vv                       GTPBP4 MUTATED GTPBP4 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              7              262
[1] 2 2
[1] FALSE

Clustering(109) Variable = ACSBG1 MUTATION ANALYSIS
D109V1, survival
                  sevent
clus2                0   1
  ACSBG1 MUTATED     7   4
  ACSBG1 WILD-TYPE 119 136
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              11              255 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               4              136 
$`ACSBG1 MUTATED`
TCGA-DA-A1HY TCGA-EB-A5SG TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2GL TCGA-EE-A2GO 
       51.12        23.15        39.62        11.31        35.54        55.69 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A3AG TCGA-FW-A3R5 
        2.73        44.25        60.49        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN 
       14.83        13.15         0.20        19.00        13.35        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        60.23         4.34        15.85 
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 
       62.79         8.55        36.85         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        32.15         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
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-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       125.65 
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        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
            0.99             0.13 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           60.49           125.65 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           35.54            16.24 
[1] "1.0 - 60.5 (35.5)"  "0.1 - 125.7 (16.2)"
[1] "hr=" "1.7"
D109V2, survival
                  sevent
clus2                0   1
  ACSBG1 MUTATED     7   4
  ACSBG1 WILD-TYPE 122 137
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              11              259 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               4              137 
$`ACSBG1 MUTATED`
TCGA-DA-A1HY TCGA-EB-A5SG TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2GL TCGA-EE-A2GO 
      117.21        68.25        56.84        46.82        79.66       126.81 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MR TCGA-EE-A3AG TCGA-FW-A3R5 
      268.73       103.20       134.40        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         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       195.02        17.92       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       158.63       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       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           22.92             0.16 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
          268.73           357.37 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           79.66            50.89 
[1] "22.9 - 268.7 (79.7)" "0.2 - 357.4 (50.9)" 
[1] "hr=" "2"  
D109V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ACSBG1 MUTATED                    1             0
  ACSBG1 WILD-TYPE                 38             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ACSBG1 MUTATED                                           2
  ACSBG1 WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  ACSBG1 MUTATED                     9
  ACSBG1 WILD-TYPE                 162
D109V4, multiclass
                                           clus
vv                                          ACSBG1 MUTATED ACSBG1 WILD-TYPE
  DISTANT METASTASIS                                     1               38
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                    9              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       3        0        1        1
  ACSBG1 WILD-TYPE          10       6      21       10       23       15
                  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        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ACSBG1 MUTATED            0          1        1
  ACSBG1 WILD-TYPE         23         45       15
D109V5, multiclass
             clus
vv            ACSBG1 MUTATED ACSBG1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  3               21
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 1               15
  STAGE IIA                2                8
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               0               13
  STAGE IIIB               0               23
  STAGE IIIC               1               45
  STAGE IV                 1               15
[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  5  3  0
  ACSBG1 WILD-TYPE    51 54 51 57
D109V6, multiclass
       clus
vv      ACSBG1 MUTATED ACSBG1 WILD-TYPE
  T0+T1              1               51
  T2                 5               54
  T3                 3               51
  T4                 0               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ACSBG1 MUTATED     7   0   2   1
  ACSBG1 WILD-TYPE 132  48  31  35
D109V7, multiclass
    clus
vv   ACSBG1 MUTATED ACSBG1 WILD-TYPE
  N0              7              132
  N1              0               48
  N2              2               31
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  ACSBG1 MUTATED    10   0   0   0   1
  ACSBG1 WILD-TYPE 234   4   3   2   7
D109V8, multiclass
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  M0              10              234
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 97 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      6    1
  ACSBG1 WILD-TYPE   97   67
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  NO               6               97
  YES              1               67
[1] 2 2
[1] FALSE
D109V10, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     1  11
  ACSBG1 WILD-TYPE  35 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      1   11
  ACSBG1 WILD-TYPE   35  228
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  NO               1               35
  YES             11              228
[1] 2 2
[1] FALSE
D109V11, continuous
D109V12, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     6   6
  ACSBG1 WILD-TYPE 100 164
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      6    6
  ACSBG1 WILD-TYPE  100  164
        clus
vv       ACSBG1 MUTATED ACSBG1 WILD-TYPE
  FEMALE              6              100
  MALE                6              164
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSBG1 MUTATED       0                         0    12
  ACSBG1 WILD-TYPE     3                         1   260
D109V13, multiclass
                           clus
vv                          ACSBG1 MUTATED ACSBG1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 12              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"
D109V14, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     0  12
  ACSBG1 WILD-TYPE   3 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      0   12
  ACSBG1 WILD-TYPE    3  257
                        clus
vv                       ACSBG1 MUTATED ACSBG1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             12              257
[1] 2 2
[1] FALSE

Clustering(110) Variable = TPTE MUTATION ANALYSIS
D110V1, survival
                sevent
clus2              0   1
  TPTE MUTATED    25  34
  TPTE WILD-TYPE 101 106
  TPTE MUTATED TPTE WILD-TYPE 
            59            207 
  TPTE MUTATED TPTE WILD-TYPE 
            34            106 
$`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        29.23        25.78 
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        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF 
        1.15         8.84        98.27        47.51         9.53         2.73 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       44.25        63.42       111.91        26.99        53.16        52.67 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A199 
       30.15        13.81        21.60        22.22        31.40         5.72 
TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZP 
       11.80         1.71        14.24         7.30        20.38        52.08 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       27.39         5.23        28.73         5.98         6.41         0.99 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 
        0.13         0.85        11.61        44.28        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        86.76        11.41        44.19         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        59.57       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        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GR 
       31.30        54.31        32.28        21.44        32.61        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.21         1.18         9.90        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       39.62         8.09         8.84         9.99         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       34.29        17.98        60.00        47.21        30.08        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       35.54        28.31        33.83        13.02        34.98        36.33 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
        2.70         6.18        29.46         7.96        14.56       125.65 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
       56.02        25.08        21.60        60.49         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        51.62         3.68        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       22.92        21.60        16.14         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       21.73        33.60        18.61        12.95        38.40        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
        9.57        36.07         6.58        17.72        78.44         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-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       22.49         5.62        18.41        85.74        15.72        64.47 
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-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-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        8.68         0.82        53.85         7.36        14.20        10.78 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.16        17.33         9.90         7.23 
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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  TPTE MUTATED TPTE WILD-TYPE 
          0.13           0.16 
  TPTE MUTATED TPTE WILD-TYPE 
        111.91         125.65 
  TPTE MUTATED TPTE WILD-TYPE 
         20.38          16.24 
[1] "0.1 - 111.9 (20.4)" "0.2 - 125.7 (16.2)"
[1] "hr=" "1.2"
D110V2, survival
                sevent
clus2              0   1
  TPTE MUTATED    26  34
  TPTE WILD-TYPE 103 107
  TPTE MUTATED TPTE WILD-TYPE 
            60            210 
  TPTE MUTATED TPTE WILD-TYPE 
            34            107 
$`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        45.30        26.89 
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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS 
      268.73       103.20        96.23       203.05       248.65       162.48 
TCGA-EE-A2MT TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A193 
       71.21        54.51        13.81        36.95        53.19        31.40 
TCGA-ER-A199 TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC 
        9.17        43.82        33.21        20.91        27.72       357.37 
TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC 
       74.73        49.48        27.02        28.73        26.73        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 
       22.92        47.54         2.04        11.74       139.89        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        86.76        11.87        62.07       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        59.57       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       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GR 
       56.35       145.12        32.94        22.62        63.81       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 
       18.18       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 
       22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       168.26        13.55        80.61 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       63.78        72.07        64.64        56.84        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       195.02        17.92       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       158.63       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      134.40        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      201.80        27.35        51.35       109.58       148.08        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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
       11.41       148.80        53.16        26.56        27.09        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       66.67       174.84        12.43        77.88         0.20         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.30         9.90         7.23       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  TPTE MUTATED TPTE WILD-TYPE 
          2.04           0.16 
  TPTE MUTATED TPTE WILD-TYPE 
        357.37         314.56 
  TPTE MUTATED TPTE WILD-TYPE 
         47.41          53.97 
[1] "2.0 - 357.4 (47.4)" "0.2 - 314.6 (54.0)"
[1] "hr=" "1.1"
D110V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TPTE MUTATED                   10             1
  TPTE WILD-TYPE                 29             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  TPTE MUTATED                                          11                  38
  TPTE WILD-TYPE                                        49                 133
D110V4, multiclass
                                           clus
vv                                          TPTE MUTATED TPTE WILD-TYPE
  DISTANT METASTASIS                                  10             29
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           11             49
  REGIONAL LYMPH NODE                                 38            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       7        2        5        7
  TPTE WILD-TYPE           7       6      17        8       19        9
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TPTE MUTATED           2         3         2         6          2          7
  TPTE WILD-TYPE         8        11         7        26         11         16
                vv
clus             STAGE IIIC STAGE IV
  TPTE MUTATED            8        2
  TPTE WILD-TYPE         38       14
D110V5, multiclass
             clus
vv            TPTE MUTATED TPTE WILD-TYPE
  I OR II NOS            3              7
  STAGE 0                0              6
  STAGE I                7             17
  STAGE IA               2              8
  STAGE IB               5             19
  STAGE II               7              9
  STAGE IIA              2              8
  STAGE IIB              3             11
  STAGE IIC              2              7
  STAGE III              6             26
  STAGE IIIA             2             11
  STAGE IIIB             7             16
  STAGE IIIC             8             38
  STAGE IV               2             14
[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 14 14 12
  TPTE WILD-TYPE    41 45 40 45
D110V6, multiclass
       clus
vv      TPTE MUTATED TPTE WILD-TYPE
  T0+T1           11             41
  T2              14             45
  T3              14             40
  T4              12             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
  TPTE MUTATED    33  12   5   5
  TPTE WILD-TYPE 106  36  28  31
D110V7, multiclass
    clus
vv   TPTE MUTATED TPTE WILD-TYPE
  N0           33            106
  N1           12             36
  N2            5             28
  N3            5             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
  TPTE MUTATED    54   1   1   0   0
  TPTE WILD-TYPE 190   3   2   2   8
D110V8, multiclass
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  M0            54            190
  M1             1              3
  M1A            1              2
  M1B            0              2
  M1C            0              8
[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 81 52
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     22   16
  TPTE WILD-TYPE   81   52
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO            22             81
  YES           16             52
[1] 2 2
[1] FALSE
D110V10, binary
                cls
clus               0   1
  TPTE MUTATED     8  52
  TPTE WILD-TYPE  28 187
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      8   52
  TPTE WILD-TYPE   28  187
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO             8             28
  YES           52            187
[1] 2 2
[1] FALSE
D110V11, continuous
D110V12, binary
                cls
clus               0   1
  TPTE MUTATED    26  34
  TPTE WILD-TYPE  80 136
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     26   34
  TPTE WILD-TYPE   80  136
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  FEMALE           26             80
  MALE             34            136
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE MUTATED       0                         0    60
  TPTE WILD-TYPE     3                         1   212
D110V13, multiclass
                           clus
vv                          TPTE MUTATED TPTE WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               60            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"
D110V14, binary
                cls
clus               0   1
  TPTE MUTATED     1  58
  TPTE WILD-TYPE   2 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      1   58
  TPTE WILD-TYPE    2  211
                        clus
vv                       TPTE MUTATED TPTE WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           58            211
[1] 2 2
[1] FALSE

Clustering(111) Variable = CLCC1 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2               0   1
  CLCC1 MUTATED     4   9
  CLCC1 WILD-TYPE 122 131
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             253 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              9             131 
$`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 
       62.79         1.08        36.30        60.00        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 
       86.76        11.41        44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15         8.55        36.85        39.62         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        32.15 
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        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL 
       34.29        17.98        47.21        30.08        19.43        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  CLCC1 MUTATED CLCC1 WILD-TYPE 
           1.08            0.13 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          70.16          125.65 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          16.47           17.33 
[1] "1.1 - 70.2 (16.5)"  "0.1 - 125.7 (17.3)"
[1] "hr=" "1.3"
D111V2, survival
                 sevent
clus2               0   1
  CLCC1 MUTATED     4   9
  CLCC1 WILD-TYPE 125 132
  CLCC1 MUTATED CLCC1 WILD-TYPE 
             13             257 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              9             132 
$`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 
       63.78         2.60        36.82       161.03        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 
       86.76        11.87        62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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        64.64        56.84        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       195.02        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        86.14        59.28        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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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-A2MR 
      158.63       203.05       167.90        47.54       248.65       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       109.58        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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  CLCC1 MUTATED CLCC1 WILD-TYPE 
           2.60            0.16 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
         161.03          357.37 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          43.43           52.01 
[1] "2.6 - 161.0 (43.4)" "0.2 - 357.4 (52.0)"
[1] "hr=" "1.7"
D111V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CLCC1 MUTATED                    0             0
  CLCC1 WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CLCC1 MUTATED                                           1                  12
  CLCC1 WILD-TYPE                                        59                 159
D111V4, multiclass
                                           clus
vv                                          CLCC1 MUTATED CLCC1 WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                  12             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
  CLCC1 MUTATED             0       0       3        0        0        0
  CLCC1 WILD-TYPE          10       6      21       10       24       16
                 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        30         11         22
                 vv
clus              STAGE IIIC STAGE IV
  CLCC1 MUTATED            3        0
  CLCC1 WILD-TYPE         43       16
D111V5, multiclass
             clus
vv            CLCC1 MUTATED CLCC1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 3              21
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               1               8
  STAGE III               2              30
  STAGE IIIA              2              11
  STAGE IIIB              1              22
  STAGE IIIC              3              43
  STAGE IV                0              16
[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    49 57 50 53
D111V6, multiclass
       clus
vv      CLCC1 MUTATED CLCC1 WILD-TYPE
  T0+T1             3              49
  T2                2              57
  T3                4              50
  T4                4              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
  CLCC1 MUTATED     5   4   2   2
  CLCC1 WILD-TYPE 134  44  31  34
D111V7, multiclass
    clus
vv   CLCC1 MUTATED CLCC1 WILD-TYPE
  N0             5             134
  N1             4              44
  N2             2              31
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  CLCC1 MUTATED    13   0   0   0   0
  CLCC1 WILD-TYPE 231   4   3   2   8
D111V8, multiclass
     clus
vv    CLCC1 MUTATED CLCC1 WILD-TYPE
  M0             13             231
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 97 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      6    4
  CLCC1 WILD-TYPE   97   64
     clus
vv    CLCC1 MUTATED CLCC1 WILD-TYPE
  NO              6              97
  YES             4              64
[1] 2 2
[1] FALSE
D111V10, binary
                 cls
clus                0   1
  CLCC1 MUTATED     1  12
  CLCC1 WILD-TYPE  35 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      1   12
  CLCC1 WILD-TYPE   35  227
     clus
vv    CLCC1 MUTATED CLCC1 WILD-TYPE
  NO              1              35
  YES            12             227
[1] 2 2
[1] FALSE
D111V11, continuous
D111V12, binary
                 cls
clus                0   1
  CLCC1 MUTATED     4   9
  CLCC1 WILD-TYPE 102 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      4    9
  CLCC1 WILD-TYPE  102  161
        clus
vv       CLCC1 MUTATED CLCC1 WILD-TYPE
  FEMALE             4             102
  MALE               9             161
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLCC1 MUTATED       0                         0    13
  CLCC1 WILD-TYPE     3                         1   259
D111V13, multiclass
                           clus
vv                          CLCC1 MUTATED CLCC1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             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"
D111V14, binary
                 cls
clus                0   1
  CLCC1 MUTATED     0  13
  CLCC1 WILD-TYPE   3 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      0   13
  CLCC1 WILD-TYPE    3  256
                        clus
vv                       CLCC1 MUTATED CLCC1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             256
[1] 2 2
[1] FALSE

Clustering(112) Variable = PPAP2B MUTATION ANALYSIS
D112V1, survival
                  sevent
clus2                0   1
  PPAP2B MUTATED     6   4
  PPAP2B WILD-TYPE 120 136
  PPAP2B MUTATED PPAP2B WILD-TYPE 
              10              256 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               4              136 
$`PPAP2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A5GO TCGA-EE-A2A0 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A3JD 
       44.19        47.87        11.31        14.56        53.16        27.35 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3R5 TCGA-GF-A6C9 
       53.85         7.36         0.99        11.61 

$`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        86.76        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR 
       32.28        21.44        32.61        25.78        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        63.42       125.65       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        60.49        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22         0.95        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A4F5 TCGA-FS-A4F8 
        8.68        27.39         0.82         5.23        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        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  PPAP2B MUTATED PPAP2B WILD-TYPE 
            0.99             0.13 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
           53.85           125.65 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
          20.955           16.900 
[1] "1.0 - 53.9 (21.0)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.4"
D112V2, survival
                  sevent
clus2                0   1
  PPAP2B MUTATED     6   4
  PPAP2B WILD-TYPE 123 137
  PPAP2B MUTATED PPAP2B WILD-TYPE 
              10              260 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
               4              137 
$`PPAP2B MUTATED`
TCGA-D3-A2JF TCGA-D3-A5GO TCGA-EE-A2A0 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A3JD 
       62.07       137.92        46.82       204.66       162.48        27.35 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FW-A3R5 TCGA-GF-A6C9 
       77.82        66.67        22.92        11.74 

$`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        86.76        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR 
       32.94        22.62        63.81        26.89       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        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       195.02        17.92       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       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       134.40        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.09        27.02        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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  PPAP2B MUTATED PPAP2B WILD-TYPE 
           11.74             0.16 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
          204.66           357.37 
  PPAP2B MUTATED PPAP2B WILD-TYPE 
          64.370           51.485 
[1] "11.7 - 204.7 (64.4)" "0.2 - 357.4 (51.5)" 
[1] "hr=" "1.5"
D112V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PPAP2B MUTATED                    3             0
  PPAP2B WILD-TYPE                 36             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PPAP2B MUTATED                                           2
  PPAP2B WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  PPAP2B MUTATED                     5
  PPAP2B WILD-TYPE                 166
D112V4, multiclass
                                           clus
vv                                          PPAP2B MUTATED PPAP2B WILD-TYPE
  DISTANT METASTASIS                                     3               36
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                    5              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
  PPAP2B MUTATED             0       0       0        1        0        2
  PPAP2B WILD-TYPE          10       6      24        9       24       14
                  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        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PPAP2B MUTATED            1          0        0
  PPAP2B WILD-TYPE         22         46       16
D112V5, multiclass
             clus
vv            PPAP2B MUTATED PPAP2B WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               24
  STAGE IA                 1                9
  STAGE IB                 0               24
  STAGE II                 2               14
  STAGE IIA                2                8
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               0               13
  STAGE IIIB               1               22
  STAGE IIIC               0               46
  STAGE IV                 0               16
[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    51 58 52 54
D112V6, multiclass
       clus
vv      PPAP2B MUTATED PPAP2B WILD-TYPE
  T0+T1              1               51
  T2                 1               58
  T3                 2               52
  T4                 3               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
  PPAP2B MUTATED     7   0   2   0
  PPAP2B WILD-TYPE 132  48  31  36
D112V7, multiclass
    clus
vv   PPAP2B MUTATED PPAP2B WILD-TYPE
  N0              7              132
  N1              0               48
  N2              2               31
  N3              0               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                M0  M1 M1A M1B M1C
  PPAP2B MUTATED     9   0   0   0   0
  PPAP2B WILD-TYPE 235   4   3   2   8
D112V8, multiclass
     clus
vv    PPAP2B MUTATED PPAP2B WILD-TYPE
  M0               9              235
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 99 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      4    1
  PPAP2B WILD-TYPE   99   67
     clus
vv    PPAP2B MUTATED PPAP2B WILD-TYPE
  NO               4               99
  YES              1               67
[1] 2 2
[1] FALSE
D112V10, binary
                  cls
clus                 0   1
  PPAP2B MUTATED     2   8
  PPAP2B WILD-TYPE  34 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      2    8
  PPAP2B WILD-TYPE   34  231
     clus
vv    PPAP2B MUTATED PPAP2B WILD-TYPE
  NO               2               34
  YES              8              231
[1] 2 2
[1] FALSE
D112V11, continuous
D112V12, binary
                  cls
clus                 0   1
  PPAP2B MUTATED     2   8
  PPAP2B WILD-TYPE 104 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      2    8
  PPAP2B WILD-TYPE  104  162
        clus
vv       PPAP2B MUTATED PPAP2B WILD-TYPE
  FEMALE              2              104
  MALE                8              162
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPAP2B MUTATED       0                         0    10
  PPAP2B WILD-TYPE     3                         1   262
D112V13, multiclass
                           clus
vv                          PPAP2B MUTATED PPAP2B WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 10              262
[1] 3 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   9
  PPAP2B WILD-TYPE   3 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPAP2B MUTATED      0    9
  PPAP2B WILD-TYPE    3  260
                        clus
vv                       PPAP2B MUTATED PPAP2B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              9              260
[1] 2 2
[1] FALSE

Clustering(113) Variable = CD300E MUTATION ANALYSIS
D113V1, survival
                  sevent
clus2                0   1
  CD300E MUTATED     6   4
  CD300E WILD-TYPE 120 136
  CD300E MUTATED CD300E WILD-TYPE 
              10              256 
  CD300E MUTATED CD300E WILD-TYPE 
               4              136 
$`CD300E MUTATED`
TCGA-DA-A1HV TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3JB 
       48.79        55.69        60.49        52.67        15.95         0.95 
TCGA-ER-A19M TCGA-FS-A1Z3 TCGA-FS-A1ZH TCGA-GF-A6C9 
       28.60        14.24        30.87        11.61 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        53.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         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        18.41        21.73        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-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        13.45        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        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        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  CD300E MUTATED CD300E WILD-TYPE 
            0.95             0.13 
  CD300E MUTATED CD300E WILD-TYPE 
           60.49           125.65 
  CD300E MUTATED CD300E WILD-TYPE 
          29.735           16.355 
[1] "0.9 - 60.5 (29.7)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1.6"
D113V2, survival
                  sevent
clus2                0   1
  CD300E MUTATED     6   4
  CD300E WILD-TYPE 123 137
  CD300E MUTATED CD300E WILD-TYPE 
              10              260 
  CD300E MUTATED CD300E WILD-TYPE 
               4              137 
$`CD300E MUTATED`
TCGA-DA-A1HV TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3JB 
       48.89       126.81       134.40        71.21        23.47       201.80 
TCGA-ER-A19M TCGA-FS-A1Z3 TCGA-FS-A1ZH TCGA-GF-A6C9 
       61.05        20.91        32.75        11.74 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       162.48        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        51.62         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-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A1ZJ 
      357.37        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-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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CD300E MUTATED CD300E WILD-TYPE 
           11.74             0.16 
  CD300E MUTATED CD300E WILD-TYPE 
          201.80           357.37 
  CD300E MUTATED CD300E WILD-TYPE 
          54.970           51.815 
[1] "11.7 - 201.8 (55.0)" "0.2 - 357.4 (51.8)" 
[1] "hr=" "1.3"
D113V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CD300E MUTATED                    2             0
  CD300E WILD-TYPE                 37             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CD300E MUTATED                                           3
  CD300E WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  CD300E MUTATED                     5
  CD300E WILD-TYPE                 166
D113V4, multiclass
                                           clus
vv                                          CD300E MUTATED CD300E WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              3               57
  REGIONAL LYMPH NODE                                    5              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
  CD300E MUTATED             0       0       1        0        2        1
  CD300E WILD-TYPE          10       6      23       10       22       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CD300E MUTATED           0         0         0         2          0
  CD300E WILD-TYPE        10        14         9        30         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CD300E MUTATED            2          0        2
  CD300E WILD-TYPE         21         46       14
D113V5, multiclass
             clus
vv            CD300E MUTATED CD300E WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 0               10
  STAGE IB                 2               22
  STAGE II                 1               15
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               0               13
  STAGE IIIB               2               21
  STAGE IIIC               0               46
  STAGE IV                 2               14
[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  3  0
  CD300E WILD-TYPE    50 56 51 57
D113V6, multiclass
       clus
vv      CD300E MUTATED CD300E WILD-TYPE
  T0+T1              2               50
  T2                 3               56
  T3                 3               51
  T4                 0               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CD300E MUTATED     5   1   3   0
  CD300E WILD-TYPE 134  47  30  36
D113V7, multiclass
    clus
vv   CD300E MUTATED CD300E WILD-TYPE
  N0              5              134
  N1              1               47
  N2              3               30
  N3              0               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                M0  M1 M1A M1B M1C
  CD300E MUTATED     7   1   0   0   1
  CD300E WILD-TYPE 237   3   3   2   7
D113V8, multiclass
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  M0               7              237
  M1               1                3
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 99 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      4    1
  CD300E WILD-TYPE   99   67
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               4               99
  YES              1               67
[1] 2 2
[1] FALSE
D113V10, binary
                  cls
clus                 0   1
  CD300E MUTATED     4   6
  CD300E WILD-TYPE  32 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      4    6
  CD300E WILD-TYPE   32  233
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               4               32
  YES              6              233
[1] 2 2
[1] FALSE
D113V11, continuous
D113V12, binary
                  cls
clus                 0   1
  CD300E MUTATED     5   5
  CD300E WILD-TYPE 101 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      5    5
  CD300E WILD-TYPE  101  165
        clus
vv       CD300E MUTATED CD300E WILD-TYPE
  FEMALE              5              101
  MALE                5              165
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD300E MUTATED       0                         0    10
  CD300E WILD-TYPE     3                         1   262
D113V13, multiclass
                           clus
vv                          CD300E MUTATED CD300E WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 10              262
[1] 3 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  10
  CD300E WILD-TYPE   3 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      0   10
  CD300E WILD-TYPE    3  259
                        clus
vv                       CD300E MUTATED CD300E WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              259
[1] 2 2
[1] FALSE

Clustering(114) Variable = ALDH5A1 MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                 0   1
  ALDH5A1 MUTATED     7   3
  ALDH5A1 WILD-TYPE 119 137
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               256 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
                3               137 
$`ALDH5A1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D9-A3Z1 TCGA-EE-A181 TCGA-EE-A29E 
       44.19        64.44        46.32         4.01         1.12        62.79 
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        86.76        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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       23.11        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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 
       60.23         4.34        15.85         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        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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-A2M5 
       55.69         5.42         1.15        13.02        34.98         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73        44.25         7.96        14.56       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
             0.99              0.13 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            64.44            125.65 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            40.26             16.19 
[1] "1.0 - 64.4 (40.3)"  "0.1 - 125.7 (16.2)"
[1] "hr=" "2.1"
D114V2, survival
                   sevent
clus2                 0   1
  ALDH5A1 MUTATED     7   3
  ALDH5A1 WILD-TYPE 122 138
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
               10               260 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
                3               138 
$`ALDH5A1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D9-A3Z1 TCGA-EE-A181 TCGA-EE-A29E 
       62.07        66.08        46.32        11.34        33.73        63.78 
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        86.76        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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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        22.29 
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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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        64.64         2.60        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       59.28        67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            11.34              0.16 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
            96.23            357.37 
  ALDH5A1 MUTATED ALDH5A1 WILD-TYPE 
           55.395            51.815 
[1] "11.3 - 96.2 (55.4)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.4"
D114V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  ALDH5A1 MUTATED                    1             0
  ALDH5A1 WILD-TYPE                 38             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ALDH5A1 MUTATED                                           2
  ALDH5A1 WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  ALDH5A1 MUTATED                     7
  ALDH5A1 WILD-TYPE                 164
D114V4, multiclass
                                           clus
vv                                          ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  DISTANT METASTASIS                                      1                38
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                58
  REGIONAL LYMPH NODE                                     7               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
  ALDH5A1 MUTATED             0       0       0        3        0        1
  ALDH5A1 WILD-TYPE          10       6      24        7       24       15
                   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        30         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  ALDH5A1 MUTATED            1          3        0
  ALDH5A1 WILD-TYPE         22         43       16
D114V5, multiclass
             clus
vv            ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   0                24
  STAGE IA                  3                 7
  STAGE IB                  0                24
  STAGE II                  1                15
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 2                30
  STAGE IIIA                0                13
  STAGE IIIB                1                22
  STAGE IIIC                3                43
  STAGE IV                  0                16
[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    49 58 52 56
D114V6, multiclass
       clus
vv      ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  T0+T1               3                49
  T2                  1                58
  T3                  2                52
  T4                  1                56
[1] 4 2
[1] TRUE
[1] "dimension of 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 134  47  32  33
D114V7, multiclass
    clus
vv   ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  N0               5               134
  N1               1                47
  N2               1                32
  N3               3                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
  ALDH5A1 MUTATED    10   0   0   0   0
  ALDH5A1 WILD-TYPE 234   4   3   2   8
D114V8, multiclass
     clus
vv    ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  M0               10               234
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 98 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      5    1
  ALDH5A1 WILD-TYPE   98   67
     clus
vv    ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  NO                5                98
  YES               1                67
[1] 2 2
[1] FALSE
D114V10, binary
                   cls
clus                  0   1
  ALDH5A1 MUTATED     0  10
  ALDH5A1 WILD-TYPE  36 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      0   10
  ALDH5A1 WILD-TYPE   36  229
     clus
vv    ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  NO                0                36
  YES              10               229
[1] 2 2
[1] FALSE
D114V11, continuous
D114V12, binary
                   cls
clus                  0   1
  ALDH5A1 MUTATED     4   6
  ALDH5A1 WILD-TYPE 102 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      4    6
  ALDH5A1 WILD-TYPE  102  164
        clus
vv       ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  FEMALE               4               102
  MALE                 6               164
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALDH5A1 MUTATED       0                         0    10
  ALDH5A1 WILD-TYPE     3                         1   262
D114V13, multiclass
                           clus
vv                          ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10               262
[1] 3 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   3 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH5A1 MUTATED      0   10
  ALDH5A1 WILD-TYPE    3  259
                        clus
vv                       ALDH5A1 MUTATED ALDH5A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               259
[1] 2 2
[1] FALSE

Clustering(115) Variable = SPRYD3 MUTATION ANALYSIS
D115V1, survival
                  sevent
clus2                0   1
  SPRYD3 MUTATED     5   3
  SPRYD3 WILD-TYPE 121 137
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               8              258 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               3              137 
$`SPRYD3 MUTATED`
TCGA-D3-A3MU TCGA-D3-A5GU TCGA-EE-A20B TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3J5 
       26.37        23.11        60.23         9.53        60.49        21.60 
TCGA-FS-A1ZK TCGA-RP-A694 
       12.89         0.69 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       13.68        17.72         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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-A20C TCGA-EE-A20F TCGA-EE-A20H 
       12.20         5.13         4.31         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        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       125.65       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        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-A1ZM 
       19.53        11.08         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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 

  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
            0.69             0.13 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
           60.49           125.65 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
          22.355           16.355 
[1] "0.7 - 60.5 (22.4)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1.5"
D115V2, survival
                  sevent
clus2                0   1
  SPRYD3 MUTATED     5   3
  SPRYD3 WILD-TYPE 124 138
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               8              262 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
               3              138 
$`SPRYD3 MUTATED`
TCGA-D3-A3MU TCGA-D3-A5GU TCGA-EE-A20B TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3J5 
       39.75       125.19       133.81        47.28       134.40        36.95 
TCGA-FS-A1ZK TCGA-RP-A694 
       23.93         0.69 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       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       158.63       203.05       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       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB 
      172.18       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       32.48        39.58         6.67         0.33 

  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
            0.69             0.16 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
          134.40           357.37 
  SPRYD3 MUTATED SPRYD3 WILD-TYPE 
          43.515           52.585 
[1] "0.7 - 134.4 (43.5)" "0.2 - 357.4 (52.6)"
[1] "hr=" "1.3"
D115V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  SPRYD3 MUTATED                    2             0
  SPRYD3 WILD-TYPE                 37             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SPRYD3 MUTATED                                           2
  SPRYD3 WILD-TYPE                                        58
                  vv
clus               REGIONAL LYMPH NODE
  SPRYD3 MUTATED                     4
  SPRYD3 WILD-TYPE                 167
D115V4, multiclass
                                           clus
vv                                          SPRYD3 MUTATED SPRYD3 WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              2               58
  REGIONAL LYMPH NODE                                    4              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
  SPRYD3 MUTATED             0       0       1        0        1        3
  SPRYD3 WILD-TYPE          10       6      23       10       23       13
                  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        31         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  SPRYD3 MUTATED            0          0        1
  SPRYD3 WILD-TYPE         23         46       15
D115V5, multiclass
             clus
vv            SPRYD3 MUTATED SPRYD3 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  1               23
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 3               13
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               31
  STAGE IIIA               1               12
  STAGE IIIB               0               23
  STAGE IIIC               0               46
  STAGE IV                 1               15
[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    51 58 51 55
D115V6, multiclass
       clus
vv      SPRYD3 MUTATED SPRYD3 WILD-TYPE
  T0+T1              1               51
  T2                 1               58
  T3                 3               51
  T4                 2               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
  SPRYD3 MUTATED     5   1   1   0
  SPRYD3 WILD-TYPE 134  47  32  36
D115V7, multiclass
    clus
vv   SPRYD3 MUTATED SPRYD3 WILD-TYPE
  N0              5              134
  N1              1               47
  N2              1               32
  N3              0               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                M0  M1 M1A M1B M1C
  SPRYD3 MUTATED     7   0   0   0   1
  SPRYD3 WILD-TYPE 237   4   3   2   7
D115V8, multiclass
     clus
vv    SPRYD3 MUTATED SPRYD3 WILD-TYPE
  M0               7              237
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 99 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      4    1
  SPRYD3 WILD-TYPE   99   67
     clus
vv    SPRYD3 MUTATED SPRYD3 WILD-TYPE
  NO               4               99
  YES              1               67
[1] 2 2
[1] FALSE
D115V10, binary
                  cls
clus                 0   1
  SPRYD3 MUTATED     1   7
  SPRYD3 WILD-TYPE  35 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      1    7
  SPRYD3 WILD-TYPE   35  232
     clus
vv    SPRYD3 MUTATED SPRYD3 WILD-TYPE
  NO               1               35
  YES              7              232
[1] 2 2
[1] FALSE
D115V11, continuous
D115V12, binary
                  cls
clus                 0   1
  SPRYD3 MUTATED     1   7
  SPRYD3 WILD-TYPE 105 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      1    7
  SPRYD3 WILD-TYPE  105  163
        clus
vv       SPRYD3 MUTATED SPRYD3 WILD-TYPE
  FEMALE              1              105
  MALE                7              163
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPRYD3 MUTATED       0                         0     8
  SPRYD3 WILD-TYPE     3                         1   264
D115V13, multiclass
                           clus
vv                          SPRYD3 MUTATED SPRYD3 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              264
[1] 3 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   8
  SPRYD3 WILD-TYPE   3 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD3 MUTATED      0    8
  SPRYD3 WILD-TYPE    3  261
                        clus
vv                       SPRYD3 MUTATED SPRYD3 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8              261
[1] 2 2
[1] FALSE

Clustering(116) Variable = MAP3K5 MUTATION ANALYSIS
D116V1, survival
                  sevent
clus2                0   1
  MAP3K5 MUTATED     8   9
  MAP3K5 WILD-TYPE 118 131
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              17              249 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
               9              131 
$`MAP3K5 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A51J TCGA-EE-A29E TCGA-EE-A2A2 TCGA-EE-A2MI 
       70.16        44.19        54.31        62.79        36.30        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A19M 
       63.42        60.49       124.31        21.60        31.40        28.60 
TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A266 
       11.74        14.24        28.73        11.61        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        86.76        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        59.57 
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 
       29.23        93.21        54.74        31.30        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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 
       36.85         1.08        39.62         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        32.15         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        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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 
       53.16        52.67         5.56       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       21.73        33.60        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-A19N TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        1.87         1.51        13.08        12.62         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-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        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           10.13             0.13 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
          124.31           125.65 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           31.40            16.01 
[1] "10.1 - 124.3 (31.4)" "0.1 - 125.7 (16.0)" 
[1] "hr=" "1.4"
D116V2, survival
                  sevent
clus2                0   1
  MAP3K5 MUTATED     8   9
  MAP3K5 WILD-TYPE 121 132
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              17              253 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
               9              132 
$`MAP3K5 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A51J TCGA-EE-A29E TCGA-EE-A2A2 TCGA-EE-A2MI 
       71.80        62.07       145.12        63.78        36.82       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-ER-A193 TCGA-ER-A19M 
       96.23       134.40       124.31        36.95        31.40        61.05 
TCGA-ER-A2NH TCGA-FS-A1Z3 TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A266 
       32.05        20.91        28.73        11.74        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        86.76        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        59.57 
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 
       45.30       174.84        55.73        56.35        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81       151.27        91.56       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        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        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 
       86.14        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       268.73       103.20        16.96       158.63       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       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           10.13             0.16 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
          204.66           357.37 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           61.05            51.62 
[1] "10.1 - 204.7 (61.0)" "0.2 - 357.4 (51.6)" 
[1] "hr=" "1"  
D116V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  MAP3K5 MUTATED                    4             0
  MAP3K5 WILD-TYPE                 35             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  MAP3K5 MUTATED                                           6
  MAP3K5 WILD-TYPE                                        54
                  vv
clus               REGIONAL LYMPH NODE
  MAP3K5 MUTATED                     9
  MAP3K5 WILD-TYPE                 162
D116V4, multiclass
                                           clus
vv                                          MAP3K5 MUTATED MAP3K5 WILD-TYPE
  DISTANT METASTASIS                                     4               35
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              6               54
  REGIONAL LYMPH NODE                                    9              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
  MAP3K5 MUTATED             0       1       1        1        2        0
  MAP3K5 WILD-TYPE          10       5      23        9       22       16
                  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        27         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAP3K5 MUTATED            2          2        2
  MAP3K5 WILD-TYPE         21         44       14
D116V5, multiclass
             clus
vv            MAP3K5 MUTATED MAP3K5 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  1               23
  STAGE IA                 1                9
  STAGE IB                 2               22
  STAGE II                 0               16
  STAGE IIA                0               10
  STAGE IIB                2               12
  STAGE IIC                0                9
  STAGE III                5               27
  STAGE IIIA               0               13
  STAGE IIIB               2               21
  STAGE IIIC               2               44
  STAGE IV                 2               14
[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    49 56 52 51
D116V6, multiclass
       clus
vv      MAP3K5 MUTATED MAP3K5 WILD-TYPE
  T0+T1              3               49
  T2                 3               56
  T3                 2               52
  T4                 6               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
  MAP3K5 MUTATED     9   5   1   1
  MAP3K5 WILD-TYPE 130  43  32  35
D116V7, multiclass
    clus
vv   MAP3K5 MUTATED MAP3K5 WILD-TYPE
  N0              9              130
  N1              5               43
  N2              1               32
  N3              1               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  MAP3K5 MUTATED    15   1   0   0   1
  MAP3K5 WILD-TYPE 229   3   3   2   7
D116V8, multiclass
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  M0              15              229
  M1               1                3
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 94 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      9    1
  MAP3K5 WILD-TYPE   94   67
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  NO               9               94
  YES              1               67
[1] 2 2
[1] FALSE
D116V10, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     5  14
  MAP3K5 WILD-TYPE  31 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      5   14
  MAP3K5 WILD-TYPE   31  225
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  NO               5               31
  YES             14              225
[1] 2 2
[1] FALSE
D116V11, continuous
D116V12, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     2  17
  MAP3K5 WILD-TYPE 104 153
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      2   17
  MAP3K5 WILD-TYPE  104  153
        clus
vv       MAP3K5 MUTATED MAP3K5 WILD-TYPE
  FEMALE              2              104
  MALE               17              153
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K5 MUTATED       0                         0    19
  MAP3K5 WILD-TYPE     3                         1   253
D116V13, multiclass
                           clus
vv                          MAP3K5 MUTATED MAP3K5 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 19              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"
D116V14, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     0  19
  MAP3K5 WILD-TYPE   3 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      0   19
  MAP3K5 WILD-TYPE    3  250
                        clus
vv                       MAP3K5 MUTATED MAP3K5 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             19              250
[1] 2 2
[1] FALSE

Clustering(117) Variable = CASP8 MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     3   3
  CASP8 WILD-TYPE 123 137
  CASP8 MUTATED CASP8 WILD-TYPE 
              6             260 
  CASP8 MUTATED CASP8 WILD-TYPE 
              3             137 
$`CASP8 MUTATED`
TCGA-D3-A2JC TCGA-EE-A29M TCGA-EE-A2M6 TCGA-EE-A3AG TCGA-EE-A3JI TCGA-FS-A1Z3 
       86.76        39.62        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        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69 
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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
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       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CASP8 MUTATED CASP8 WILD-TYPE 
          14.24            0.13 
  CASP8 MUTATED CASP8 WILD-TYPE 
          98.27          125.65 
  CASP8 MUTATED CASP8 WILD-TYPE 
         36.610          16.355 
[1] "14.2 - 98.3 (36.6)" "0.1 - 125.7 (16.4)"
[1] "hr=" "1.7"
D117V2, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     3   3
  CASP8 WILD-TYPE 126 138
  CASP8 MUTATED CASP8 WILD-TYPE 
              6             264 
  CASP8 MUTATED CASP8 WILD-TYPE 
              3             138 
$`CASP8 MUTATED`
TCGA-D3-A2JC TCGA-EE-A29M TCGA-EE-A2M6 TCGA-EE-A3AG TCGA-EE-A3JI TCGA-FS-A1Z3 
       86.76        56.84       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        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       53.19       201.80        27.35        51.35       109.58        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  CASP8 MUTATED CASP8 WILD-TYPE 
          20.91            0.16 
  CASP8 MUTATED CASP8 WILD-TYPE 
         148.08          357.37 
  CASP8 MUTATED CASP8 WILD-TYPE 
         71.800          51.485 
[1] "20.9 - 148.1 (71.8)" "0.2 - 357.4 (51.5)" 
[1] "hr=" "1.1"
D117V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CASP8 MUTATED                    3             0
  CASP8 WILD-TYPE                 36             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CASP8 MUTATED                                           1                   5
  CASP8 WILD-TYPE                                        59                 166
D117V4, multiclass
                                           clus
vv                                          CASP8 MUTATED CASP8 WILD-TYPE
  DISTANT METASTASIS                                    3              36
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                   5             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
  CASP8 MUTATED             2       0       2        0        1        0
  CASP8 WILD-TYPE           8       6      22       10       23       16
                 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        30         13         23
                 vv
clus              STAGE IIIC STAGE IV
  CASP8 MUTATED            0        2
  CASP8 WILD-TYPE         46       14
D117V5, multiclass
             clus
vv            CASP8 MUTATED CASP8 WILD-TYPE
  I OR II NOS             2               8
  STAGE 0                 0               6
  STAGE I                 2              22
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              0              46
  STAGE IV                2              14
[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    49 56 54 57
D117V6, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1             3              49
  T2                3              56
  T3                0              54
  T4                0              57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CASP8 MUTATED     6   0   2   0
  CASP8 WILD-TYPE 133  48  31  36
D117V7, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             6             133
  N1             0              48
  N2             2              31
  N3             0              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               M0  M1 M1A M1B M1C
  CASP8 MUTATED     7   1   0   0   1
  CASP8 WILD-TYPE 237   3   3   2   7
D117V8, multiclass
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  M0              7             237
  M1              1               3
  M1A             0               3
  M1B             0               2
  M1C             1               7
[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 100  68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3    0
  CASP8 WILD-TYPE  100   68
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              3             100
  YES             0              68
[1] 2 2
[1] FALSE
D117V10, binary
                 cls
clus                0   1
  CASP8 MUTATED     3   6
  CASP8 WILD-TYPE  33 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3    6
  CASP8 WILD-TYPE   33  233
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              3              33
  YES             6             233
[1] 2 2
[1] FALSE
D117V11, continuous
D117V12, binary
                 cls
clus                0   1
  CASP8 MUTATED     5   4
  CASP8 WILD-TYPE 101 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5    4
  CASP8 WILD-TYPE  101  166
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             5             101
  MALE               4             166
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED       0                         0     9
  CASP8 WILD-TYPE     3                         1   263
D117V13, multiclass
                           clus
vv                          CASP8 MUTATED CASP8 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V14, binary
                 cls
clus                0   1
  CASP8 MUTATED     0   9
  CASP8 WILD-TYPE   3 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0    9
  CASP8 WILD-TYPE    3  260
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             260
[1] 2 2
[1] FALSE

Clustering(118) Variable = SNCAIP MUTATION ANALYSIS
D118V1, survival
                  sevent
clus2                0   1
  SNCAIP MUTATED    26  20
  SNCAIP WILD-TYPE 100 120
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              46              220 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              20              120 
$`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        93.21 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
       25.78        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 
       15.85        11.15        62.79        39.62        49.22        51.12 
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        55.69         9.53 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD 
       60.49        53.16        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 TCGA-RP-A694 
        6.41         0.99        10.13         0.69 

$`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 
       86.76        11.41        44.19         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        59.57       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        29.23        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
       54.31        32.28        21.44        32.61        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
       17.72        23.11        21.93        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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       60.23         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55        36.85         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-A2A0 
        8.84         9.99         2.43        32.15         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.30         9.67        36.33        17.98        60.00        47.21 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        28.31         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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        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       125.65       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        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        13.81        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14         0.95        18.41        21.73        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-A19G TCGA-ER-A19H TCGA-ER-A19J 
       25.18         3.78         3.52       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
        8.81        40.64         8.68         0.82         5.23        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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       12.16        14.70         5.79         0.33 

  SNCAIP MUTATED SNCAIP WILD-TYPE 
            0.69             0.13 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          110.79           125.65 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          27.735           15.620 
[1] "0.7 - 110.8 (27.7)" "0.1 - 125.7 (15.6)"
[1] "hr=" "1.5"
D118V2, survival
                  sevent
clus2                0   1
  SNCAIP MUTATED    26  20
  SNCAIP WILD-TYPE 103 121
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              46              224 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
              20              121 
$`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       174.84 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
       26.89       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 
       91.56        13.97        63.78        56.84       102.90        59.28 
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       126.81        47.28 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD 
      134.40       162.48        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 TCGA-RP-A694 
       49.45        22.92        10.13         0.69 

$`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 
       86.76        11.87        62.07       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        59.57       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        45.30        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
      145.12        32.94        22.62        63.81       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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 
       22.29        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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81       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        64.64 
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       195.02        17.92        46.82        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL 
       86.14       314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      203.05       167.90        47.54       248.65        43.23        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        51.62         3.68        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        51.35       109.58       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-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        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-A1ZT 
       23.93       101.26        74.73       133.55        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       26.56        27.09        27.02        77.82        66.67       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-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 
        6.67         0.33 

  SNCAIP MUTATED SNCAIP WILD-TYPE 
            0.69             0.16 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          194.83           357.37 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          51.335           51.815 
[1] "0.7 - 194.8 (51.3)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.1"
D118V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  SNCAIP MUTATED                    7             2
  SNCAIP WILD-TYPE                 32             3
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SNCAIP MUTATED                                          13
  SNCAIP WILD-TYPE                                        47
                  vv
clus               REGIONAL LYMPH NODE
  SNCAIP MUTATED                    26
  SNCAIP WILD-TYPE                 145
D118V4, multiclass
                                           clus
vv                                          SNCAIP MUTATED SNCAIP WILD-TYPE
  DISTANT METASTASIS                                     7               32
  PRIMARY TUMOR                                          2                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             13               47
  REGIONAL LYMPH NODE                                   26              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
  SNCAIP MUTATED             1       2       3        3        6        4
  SNCAIP WILD-TYPE           9       4      21        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        28         11
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  SNCAIP MUTATED            5          8        5
  SNCAIP WILD-TYPE         18         38       11
D118V5, multiclass
             clus
vv            SNCAIP MUTATED SNCAIP WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  2                4
  STAGE I                  3               21
  STAGE IA                 3                7
  STAGE IB                 6               18
  STAGE II                 4               12
  STAGE IIA                2                8
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                4               28
  STAGE IIIA               2               11
  STAGE IIIB               5               18
  STAGE IIIC               8               38
  STAGE IV                 5               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
  SNCAIP MUTATED      11 13  9  5
  SNCAIP WILD-TYPE    41 46 45 52
D118V6, multiclass
       clus
vv      SNCAIP MUTATED SNCAIP WILD-TYPE
  T0+T1             11               41
  T2                13               46
  T3                 9               45
  T4                 5               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
  SNCAIP MUTATED    25  10   5   5
  SNCAIP WILD-TYPE 114  38  28  31
D118V7, multiclass
    clus
vv   SNCAIP MUTATED SNCAIP WILD-TYPE
  N0             25              114
  N1             10               38
  N2              5               28
  N3              5               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
  SNCAIP MUTATED    42   1   0   1   3
  SNCAIP WILD-TYPE 202   3   3   1   5
D118V8, multiclass
     clus
vv    SNCAIP MUTATED SNCAIP WILD-TYPE
  M0              42              202
  M1               1                3
  M1A              0                3
  M1B              1                1
  M1C              3                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"
D118V9, binary
                  cls
clus                0  1
  SNCAIP MUTATED   19 10
  SNCAIP WILD-TYPE 84 58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED     19   10
  SNCAIP WILD-TYPE   84   58
     clus
vv    SNCAIP MUTATED SNCAIP WILD-TYPE
  NO              19               84
  YES             10               58
[1] 2 2
[1] FALSE
D118V10, binary
                  cls
clus                 0   1
  SNCAIP MUTATED     8  40
  SNCAIP WILD-TYPE  28 199
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED      8   40
  SNCAIP WILD-TYPE   28  199
     clus
vv    SNCAIP MUTATED SNCAIP WILD-TYPE
  NO               8               28
  YES             40              199
[1] 2 2
[1] FALSE
D118V11, continuous
D118V12, binary
                  cls
clus                 0   1
  SNCAIP MUTATED    15  33
  SNCAIP WILD-TYPE  91 137
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED     15   33
  SNCAIP WILD-TYPE   91  137
        clus
vv       SNCAIP MUTATED SNCAIP WILD-TYPE
  FEMALE             15               91
  MALE               33              137
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SNCAIP MUTATED       0                         0    48
  SNCAIP WILD-TYPE     3                         1   224
D118V13, multiclass
                           clus
vv                          SNCAIP MUTATED SNCAIP WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 48              224
[1] 3 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  48
  SNCAIP WILD-TYPE   3 221
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED      0   48
  SNCAIP WILD-TYPE    3  221
                        clus
vv                       SNCAIP MUTATED SNCAIP WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             48              221
[1] 2 2
[1] FALSE

Clustering(119) Variable = HLA-DRA MUTATION ANALYSIS
D119V1, survival
                   sevent
clus2                 0   1
  HLA-DRA MUTATED     8   4
  HLA-DRA WILD-TYPE 118 136
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               12               254 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                4               136 
$`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        62.79         8.84 
TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MR TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GF-A6C9 
       55.69        14.56        60.49        28.73         0.99        11.61 

$`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        86.76        11.41        44.19 
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        59.57 
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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23        15.85         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        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        1.08        39.62         9.50        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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        63.42       125.65 
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        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
             0.99              0.13 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
           114.67            125.65 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
           42.210            16.355 
[1] "1.0 - 114.7 (42.2)" "0.1 - 125.7 (16.4)"
[1] "hr=" "2.1"
D119V2, survival
                   sevent
clus2                 0   1
  HLA-DRA MUTATED     8   4
  HLA-DRA WILD-TYPE 121 137
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
               12               258 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
                4               137 
$`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        63.78        14.47 
TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MR TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GF-A6C9 
      126.81       204.66       134.40        28.73        22.92        11.74 

$`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        86.76        11.87        62.07 
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        59.57 
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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81        91.56       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        64.64         2.60        56.84 
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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96        96.23       158.63       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       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            11.74              0.16 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
           204.66            357.37 
  HLA-DRA MUTATED HLA-DRA WILD-TYPE 
            68.94             51.12 
[1] "11.7 - 204.7 (68.9)" "0.2 - 357.4 (51.1)" 
[1] "hr=" "1.9"
D119V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  HLA-DRA MUTATED                    2             0
  HLA-DRA WILD-TYPE                 37             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  HLA-DRA MUTATED                                           4
  HLA-DRA WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  HLA-DRA MUTATED                     6
  HLA-DRA WILD-TYPE                 165
D119V4, multiclass
                                           clus
vv                                          HLA-DRA MUTATED HLA-DRA WILD-TYPE
  DISTANT METASTASIS                                      2                37
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                56
  REGIONAL LYMPH NODE                                     6               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
  HLA-DRA MUTATED             0       1       1        0        1        1
  HLA-DRA WILD-TYPE          10       5      23       10       23       15
                   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        30         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  HLA-DRA MUTATED            2          2        0
  HLA-DRA WILD-TYPE         21         44       16
D119V5, multiclass
             clus
vv            HLA-DRA MUTATED HLA-DRA WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   1                23
  STAGE IA                  0                10
  STAGE IB                  1                23
  STAGE II                  1                15
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 0                 9
  STAGE III                 2                30
  STAGE IIIA                0                13
  STAGE IIIB                2                21
  STAGE IIIC                2                44
  STAGE IV                  0                16
[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    52 57 51 54
D119V6, multiclass
       clus
vv      HLA-DRA MUTATED HLA-DRA WILD-TYPE
  T0+T1               0                52
  T2                  2                57
  T3                  3                51
  T4                  3                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
  HLA-DRA MUTATED     6   3   1   1
  HLA-DRA WILD-TYPE 133  45  32  35
D119V7, multiclass
    clus
vv   HLA-DRA MUTATED HLA-DRA WILD-TYPE
  N0               6               133
  N1               3                45
  N2               1                32
  N3               1                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  HLA-DRA MUTATED    11   0   0   0   0
  HLA-DRA WILD-TYPE 233   4   3   2   8
D119V8, multiclass
     clus
vv    HLA-DRA MUTATED HLA-DRA WILD-TYPE
  M0               11               233
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 98 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      5    2
  HLA-DRA WILD-TYPE   98   66
     clus
vv    HLA-DRA MUTATED HLA-DRA WILD-TYPE
  NO                5                98
  YES               2                66
[1] 2 2
[1] FALSE
D119V10, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     1  11
  HLA-DRA WILD-TYPE  35 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      1   11
  HLA-DRA WILD-TYPE   35  228
     clus
vv    HLA-DRA MUTATED HLA-DRA WILD-TYPE
  NO                1                35
  YES              11               228
[1] 2 2
[1] FALSE
D119V11, continuous
D119V12, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     4   8
  HLA-DRA WILD-TYPE 102 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      4    8
  HLA-DRA WILD-TYPE  102  162
        clus
vv       HLA-DRA MUTATED HLA-DRA WILD-TYPE
  FEMALE               4               102
  MALE                 8               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-DRA MUTATED       0                         0    12
  HLA-DRA WILD-TYPE     3                         1   260
D119V13, multiclass
                           clus
vv                          HLA-DRA MUTATED HLA-DRA WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  12               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"
D119V14, binary
                   cls
clus                  0   1
  HLA-DRA MUTATED     1  11
  HLA-DRA WILD-TYPE   2 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HLA-DRA MUTATED      1   11
  HLA-DRA WILD-TYPE    2  258
                        clus
vv                       HLA-DRA MUTATED HLA-DRA WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              11               258
[1] 2 2
[1] FALSE

Clustering(120) Variable = ACTC1 MUTATION ANALYSIS
D120V1, survival
                 sevent
clus2               0   1
  ACTC1 MUTATED     7   8
  ACTC1 WILD-TYPE 119 132
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             251 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              8             132 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        9.21         1.18         7.99        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55        36.85        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46         2.73         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      125.65        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15         8.68        27.39         0.82         5.23 
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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        0.85        11.61        44.28        31.33        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  ACTC1 MUTATED ACTC1 WILD-TYPE 
           0.99            0.13 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
         111.91          125.65 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
          10.13           17.33 
[1] "1.0 - 111.9 (10.1)" "0.1 - 125.7 (17.3)"
[1] "hr=" "1"  
D120V2, survival
                 sevent
clus2               0   1
  ACTC1 MUTATED     7   8
  ACTC1 WILD-TYPE 122 133
  ACTC1 MUTATED ACTC1 WILD-TYPE 
             15             255 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              8             133 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
       56.84        18.61        56.42        37.35        14.47       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
      268.73        16.96       204.66        96.23       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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-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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      139.89       117.93        64.44        62.79        32.48        39.58 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  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           50.89 
[1] "2.6 - 203.1 (64.1)" "0.2 - 357.4 (50.9)"
[1] "hr=" "1"  
D120V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ACTC1 MUTATED                    3             0
  ACTC1 WILD-TYPE                 36             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ACTC1 MUTATED                                           4                   8
  ACTC1 WILD-TYPE                                        56                 163
D120V4, multiclass
                                           clus
vv                                          ACTC1 MUTATED ACTC1 WILD-TYPE
  DISTANT METASTASIS                                    3              36
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             4              56
  REGIONAL LYMPH NODE                                   8             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
  ACTC1 MUTATED             1       0       2        0        0        1
  ACTC1 WILD-TYPE           9       6      22       10       24       15
                 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        30         13         23
                 vv
clus              STAGE IIIC STAGE IV
  ACTC1 MUTATED            3        1
  ACTC1 WILD-TYPE         43       15
D120V5, multiclass
             clus
vv            ACTC1 MUTATED ACTC1 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 2              22
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               1               9
  STAGE IIB               2              12
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              3              43
  STAGE IV                1              15
[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    52 55 50 54
D120V6, multiclass
       clus
vv      ACTC1 MUTATED ACTC1 WILD-TYPE
  T0+T1             0              52
  T2                4              55
  T3                4              50
  T4                3              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
  ACTC1 MUTATED     7   2   1   3
  ACTC1 WILD-TYPE 132  46  32  33
D120V7, multiclass
    clus
vv   ACTC1 MUTATED ACTC1 WILD-TYPE
  N0             7             132
  N1             2              46
  N2             1              32
  N3             3              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
  ACTC1 MUTATED    12   0   1   0   0
  ACTC1 WILD-TYPE 232   4   2   2   8
D120V8, multiclass
     clus
vv    ACTC1 MUTATED ACTC1 WILD-TYPE
  M0             12             232
  M1              0               4
  M1A             1               2
  M1B             0               2
  M1C             0               8
[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 100  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      3    5
  ACTC1 WILD-TYPE  100   63
     clus
vv    ACTC1 MUTATED ACTC1 WILD-TYPE
  NO              3             100
  YES             5              63
[1] 2 2
[1] FALSE
D120V10, binary
                 cls
clus                0   1
  ACTC1 MUTATED     2  13
  ACTC1 WILD-TYPE  34 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      2   13
  ACTC1 WILD-TYPE   34  226
     clus
vv    ACTC1 MUTATED ACTC1 WILD-TYPE
  NO              2              34
  YES            13             226
[1] 2 2
[1] FALSE
D120V11, continuous
D120V12, binary
                 cls
clus                0   1
  ACTC1 MUTATED     2  13
  ACTC1 WILD-TYPE 104 157
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      2   13
  ACTC1 WILD-TYPE  104  157
        clus
vv       ACTC1 MUTATED ACTC1 WILD-TYPE
  FEMALE             2             104
  MALE              13             157
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACTC1 MUTATED       0                         0    15
  ACTC1 WILD-TYPE     3                         1   257
D120V13, multiclass
                           clus
vv                          ACTC1 MUTATED ACTC1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                15             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"
D120V14, binary
                 cls
clus                0   1
  ACTC1 MUTATED     0  15
  ACTC1 WILD-TYPE   3 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      0   15
  ACTC1 WILD-TYPE    3  254
                        clus
vv                       ACTC1 MUTATED ACTC1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            15             254
[1] 2 2
[1] FALSE

Clustering(121) Variable = ELOVL3 MUTATION ANALYSIS
D121V1, survival
                  sevent
clus2                0   1
  ELOVL3 MUTATED     2   3
  ELOVL3 WILD-TYPE 124 137
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              261 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               3              137 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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-A20C 
        1.12        12.20         5.13         4.31        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71         5.62        85.74        15.72        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-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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
            1.35             0.13 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
           63.42           125.65 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
           18.41            16.47 
[1] "1.4 - 63.4 (18.4)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.3"
D121V2, survival
                  sevent
clus2                0   1
  ELOVL3 MUTATED     2   3
  ELOVL3 WILD-TYPE 127 138
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               5              265 
  ELOVL3 MUTATED ELOVL3 WILD-TYPE 
               3              138 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08         7.79        27.72       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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  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            52.01 
[1] "14.7 - 96.2 (49.5)" "0.2 - 357.4 (52.0)"
[1] "hr=" "1.3"
D121V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  ELOVL3 MUTATED                    2             0
  ELOVL3 WILD-TYPE                 37             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  ELOVL3 MUTATED                                           0
  ELOVL3 WILD-TYPE                                        60
                  vv
clus               REGIONAL LYMPH NODE
  ELOVL3 MUTATED                     3
  ELOVL3 WILD-TYPE                 168
D121V4, multiclass
                                           clus
vv                                          ELOVL3 MUTATED ELOVL3 WILD-TYPE
  DISTANT METASTASIS                                     2               37
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              0               60
  REGIONAL LYMPH NODE                                    3              168
[1] 4 2
[1] 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      24       10       23       15
                  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        31         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ELOVL3 MUTATED            1          1        0
  ELOVL3 WILD-TYPE         22         45       16
D121V5, multiclass
             clus
vv            ELOVL3 MUTATED ELOVL3 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  0                6
  STAGE I                  0               24
  STAGE IA                 0               10
  STAGE IB                 1               23
  STAGE II                 1               15
  STAGE IIA                0               10
  STAGE IIB                0               14
  STAGE IIC                0                9
  STAGE III                1               31
  STAGE IIIA               0               13
  STAGE IIIB               1               22
  STAGE IIIC               1               45
  STAGE IV                 0               16
[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    52 57 53 55
D121V6, multiclass
       clus
vv      ELOVL3 MUTATED ELOVL3 WILD-TYPE
  T0+T1              0               52
  T2                 2               57
  T3                 1               53
  T4                 2               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
  ELOVL3 MUTATED     3   2   0   0
  ELOVL3 WILD-TYPE 136  46  33  36
D121V7, multiclass
    clus
vv   ELOVL3 MUTATED ELOVL3 WILD-TYPE
  N0              3              136
  N1              2               46
  N2              0               33
  N3              0               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                M0  M1 M1A M1B M1C
  ELOVL3 MUTATED     5   0   0   0   0
  ELOVL3 WILD-TYPE 239   4   3   2   8
D121V8, multiclass
     clus
vv    ELOVL3 MUTATED ELOVL3 WILD-TYPE
  M0               5              239
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 100  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      3    2
  ELOVL3 WILD-TYPE  100   66
     clus
vv    ELOVL3 MUTATED ELOVL3 WILD-TYPE
  NO               3              100
  YES              2               66
[1] 2 2
[1] FALSE
D121V10, binary
                  cls
clus                 0   1
  ELOVL3 MUTATED     0   5
  ELOVL3 WILD-TYPE  36 234
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      0    5
  ELOVL3 WILD-TYPE   36  234
     clus
vv    ELOVL3 MUTATED ELOVL3 WILD-TYPE
  NO               0               36
  YES              5              234
[1] 2 2
[1] FALSE
D121V11, continuous
D121V12, binary
                  cls
clus                 0   1
  ELOVL3 MUTATED     1   4
  ELOVL3 WILD-TYPE 105 166
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      1    4
  ELOVL3 WILD-TYPE  105  166
        clus
vv       ELOVL3 MUTATED ELOVL3 WILD-TYPE
  FEMALE              1              105
  MALE                4              166
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELOVL3 MUTATED       0                         0     5
  ELOVL3 WILD-TYPE     3                         1   267
D121V13, multiclass
                           clus
vv                          ELOVL3 MUTATED ELOVL3 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  5              267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V14, binary
                  cls
clus                 0   1
  ELOVL3 MUTATED     0   5
  ELOVL3 WILD-TYPE   3 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL3 MUTATED      0    5
  ELOVL3 WILD-TYPE    3  264
                        clus
vv                       ELOVL3 MUTATED ELOVL3 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5              264
[1] 2 2
[1] FALSE

Clustering(122) Variable = THSD7B MUTATION ANALYSIS
D122V1, survival
                  sevent
clus2               0  1
  THSD7B MUTATED   43 42
  THSD7B WILD-TYPE 83 98
  THSD7B MUTATED THSD7B WILD-TYPE 
              85              181 
  THSD7B MUTATED THSD7B WILD-TYPE 
              42               98 
$`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        44.19        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        29.23        93.21        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-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20H 
       13.35         1.12         1.35         4.31         4.34         9.21 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        7.99        11.15        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GB 
       39.62         9.50         9.99         2.43        49.22        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GP 
       34.29        17.98        30.08        19.43        28.31         5.42 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ 
        1.15         8.84        47.51         9.53        14.56        63.42 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
      111.91        25.08        26.99        60.49        53.16         5.56 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JA 
      124.31        51.62        15.95         3.22        21.60        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19A 
        0.95        27.35        33.60        31.40        38.40        76.41 
TCGA-ER-A19M TCGA-ER-A2NC TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZP 
       28.60        11.80        85.74        23.80         7.33        52.08 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3R5 
       40.64        27.39        53.85        28.73         6.41         0.99 
TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 TCGA-QB-A6FS TCGA-RP-A693 
        0.16        11.61        10.13        15.42         5.79         0.33 
TCGA-RP-A694 
        0.69 

$`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        86.76        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        59.57       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        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87        13.68        17.72         4.01        21.93 
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        23.15        19.00 
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        60.23        15.85         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        32.15         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
       36.30         9.67        36.33        60.00        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        55.69        13.02        34.98        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       98.27         2.70         6.18        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AB 
        7.96       125.65        56.02        21.60        52.67       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 
        3.68        30.15        13.81        12.72        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       16.14        18.41        21.73        18.61        12.95         5.72 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71         5.62        18.41        15.72        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       11.01        14.24        15.52         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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       12.89        47.38         8.65         8.81        49.15         8.68 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        0.82         5.23         7.36        14.20        10.78         5.98 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.13        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        0.85        44.28        31.33        84.72        16.24        12.16 
TCGA-GN-A26D 
       14.70 

  THSD7B MUTATED THSD7B WILD-TYPE 
            0.16             0.13 
  THSD7B MUTATED THSD7B WILD-TYPE 
          124.31           125.65 
  THSD7B MUTATED THSD7B WILD-TYPE 
           23.80            15.72 
[1] "0.2 - 124.3 (23.8)" "0.1 - 125.7 (15.7)"
[1] "hr=" "1.2"
D122V2, survival
                  sevent
clus2               0  1
  THSD7B MUTATED   44 42
  THSD7B WILD-TYPE 85 99
  THSD7B MUTATED THSD7B WILD-TYPE 
              86              184 
  THSD7B MUTATED THSD7B WILD-TYPE 
              42               99 
$`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        62.07        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        45.30       174.84       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        17.29        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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 
        2.60        56.84        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 
       59.28        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       134.40       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
       53.26       124.31        51.62        23.47       172.18        36.95 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 
       53.19       201.80        27.35       148.08        31.40        50.76 
TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A2NC TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z7 
       77.75        61.05        43.82       174.21       202.65         7.79 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC 
       74.73        53.16        49.48        77.82        28.73        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 TCGA-QB-A6FS 
       22.92         0.16        11.74        10.13        62.79         6.67 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

$`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        86.76        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        59.57       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        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        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       133.81        91.56 
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 
      195.02        17.92        46.82        36.82        39.29        86.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
      161.03       208.04        54.74        79.66        90.97       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM 
      103.27       268.73       103.20        16.96       158.63       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       43.23        71.21       122.73         3.68        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH 
      138.81       127.20        64.08        34.32        51.35       109.58 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94         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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.72       216.92        48.59       228.59        20.91        28.08 
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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
       11.41       148.80        26.56        27.09        27.02        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-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         7.23         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        64.44        32.48        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 
          58.060           48.215 
[1] "0.2 - 314.6 (58.1)" "0.2 - 357.4 (48.2)"
[1] "hr=" "1.2"
D122V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  THSD7B MUTATED                   16             1
  THSD7B WILD-TYPE                 23             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  THSD7B MUTATED                                          22
  THSD7B WILD-TYPE                                        38
                  vv
clus               REGIONAL LYMPH NODE
  THSD7B MUTATED                    49
  THSD7B WILD-TYPE                 122
D122V4, multiclass
                                           clus
vv                                          THSD7B MUTATED THSD7B WILD-TYPE
  DISTANT METASTASIS                                    16               23
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             22               38
  REGIONAL LYMPH NODE                                   49              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
  THSD7B MUTATED             4       1       7        6        9        7
  THSD7B WILD-TYPE           6       5      17        4       15        9
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  THSD7B MUTATED           2         6         1        14          4
  THSD7B WILD-TYPE         8         8         8        18          9
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  THSD7B MUTATED           10          9        5
  THSD7B WILD-TYPE         13         37       11
D122V5, multiclass
             clus
vv            THSD7B MUTATED THSD7B WILD-TYPE
  I OR II NOS              4                6
  STAGE 0                  1                5
  STAGE I                  7               17
  STAGE IA                 6                4
  STAGE IB                 9               15
  STAGE II                 7                9
  STAGE IIA                2                8
  STAGE IIB                6                8
  STAGE IIC                1                8
  STAGE III               14               18
  STAGE IIIA               4                9
  STAGE IIIB              10               13
  STAGE IIIC               9               37
  STAGE IV                 5               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
  THSD7B MUTATED      18 25 17 15
  THSD7B WILD-TYPE    34 34 37 42
D122V6, multiclass
       clus
vv      THSD7B MUTATED THSD7B WILD-TYPE
  T0+T1             18               34
  T2                25               34
  T3                17               37
  T4                15               42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  THSD7B MUTATED   46 19 13  4
  THSD7B WILD-TYPE 93 29 20 32
D122V7, multiclass
    clus
vv   THSD7B MUTATED THSD7B WILD-TYPE
  N0             46               93
  N1             19               29
  N2             13               20
  N3              4               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
  THSD7B MUTATED    81   1   0   0   4
  THSD7B WILD-TYPE 163   3   3   2   4
D122V8, multiclass
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  M0              81              163
  M1               1                3
  M1A              0                3
  M1B              0                2
  M1C              4                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 65 51
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     38   17
  THSD7B WILD-TYPE   65   51
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  NO              38               65
  YES             17               51
[1] 2 2
[1] FALSE
D122V10, binary
                  cls
clus                 0   1
  THSD7B MUTATED    14  74
  THSD7B WILD-TYPE  22 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     14   74
  THSD7B WILD-TYPE   22  165
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  NO              14               22
  YES             74              165
[1] 2 2
[1] FALSE
D122V11, continuous
D122V12, binary
                  cls
clus                 0   1
  THSD7B MUTATED    26  62
  THSD7B WILD-TYPE  80 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     26   62
  THSD7B WILD-TYPE   80  108
        clus
vv       THSD7B MUTATED THSD7B WILD-TYPE
  FEMALE             26               80
  MALE               62              108
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THSD7B MUTATED       0                         0    88
  THSD7B WILD-TYPE     3                         1   184
D122V13, multiclass
                           clus
vv                          THSD7B MUTATED THSD7B WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 88              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"
D122V14, binary
                  cls
clus                 0   1
  THSD7B MUTATED     0  87
  THSD7B WILD-TYPE   3 182
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED      0   87
  THSD7B WILD-TYPE    3  182
                        clus
vv                       THSD7B MUTATED THSD7B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             87              182
[1] 2 2
[1] FALSE

Clustering(123) Variable = SLC27A5 MUTATION ANALYSIS
D123V1, survival
                   sevent
clus2                 0   1
  SLC27A5 MUTATED     4   4
  SLC27A5 WILD-TYPE 122 136
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               258 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                4               136 
$`SLC27A5 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AG 
       46.98        25.78        11.57         9.53        51.62        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.28        21.44        32.61        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        60.23         4.34        15.85         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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        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       125.65       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        60.49        53.16        52.67 
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-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       22.22         0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       14.20        10.78         5.98         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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
             6.41              0.13 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
            51.62            125.65 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           20.865            16.900 
[1] "6.4 - 51.6 (20.9)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.1"
D123V2, survival
                   sevent
clus2                 0   1
  SLC27A5 MUTATED     4   4
  SLC27A5 WILD-TYPE 125 137
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                8               262 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                4               137 
$`SLC27A5 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AG 
       46.98        26.89        29.82        47.28        51.62        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.94        22.62        63.81       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73         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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       109.58        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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
            23.47              0.16 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           148.08            357.37 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           47.130            53.225 
[1] "23.5 - 148.1 (47.1)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1.3"
D123V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  SLC27A5 MUTATED                    0             0
  SLC27A5 WILD-TYPE                 39             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  SLC27A5 MUTATED                                           2
  SLC27A5 WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  SLC27A5 MUTATED                     6
  SLC27A5 WILD-TYPE                 165
D123V4, multiclass
                                           clus
vv                                          SLC27A5 MUTATED SLC27A5 WILD-TYPE
  DISTANT METASTASIS                                      0                39
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                58
  REGIONAL LYMPH NODE                                     6               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
  SLC27A5 MUTATED             0       0       1        1        0        1
  SLC27A5 WILD-TYPE          10       6      23        9       24       15
                   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        29         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC27A5 MUTATED            0          1        0
  SLC27A5 WILD-TYPE         23         45       16
D123V5, multiclass
             clus
vv            SLC27A5 MUTATED SLC27A5 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   1                23
  STAGE IA                  1                 9
  STAGE IB                  0                24
  STAGE II                  1                15
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 0                 9
  STAGE III                 3                29
  STAGE IIIA                0                13
  STAGE IIIB                0                23
  STAGE IIIC                1                45
  STAGE IV                  0                16
[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    48 58 52 56
D123V6, multiclass
       clus
vv      SLC27A5 MUTATED SLC27A5 WILD-TYPE
  T0+T1               4                48
  T2                  1                58
  T3                  2                52
  T4                  1                56
[1] 4 2
[1] TRUE
[1] "dimension of 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 135  46  31  36
D123V7, multiclass
    clus
vv   SLC27A5 MUTATED SLC27A5 WILD-TYPE
  N0               4               135
  N1               2                46
  N2               2                31
  N3               0                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                 M0  M1 M1A M1B M1C
  SLC27A5 MUTATED     8   0   0   0   0
  SLC27A5 WILD-TYPE 236   4   3   2   8
D123V8, multiclass
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  M0                8               236
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               0                 8
[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 100  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    2
  SLC27A5 WILD-TYPE  100   66
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  NO                3               100
  YES               2                66
[1] 2 2
[1] FALSE
D123V10, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     3   5
  SLC27A5 WILD-TYPE  33 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    5
  SLC27A5 WILD-TYPE   33  234
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  NO                3                33
  YES               5               234
[1] 2 2
[1] FALSE
D123V11, continuous
D123V12, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     3   5
  SLC27A5 WILD-TYPE 103 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    5
  SLC27A5 WILD-TYPE  103  165
        clus
vv       SLC27A5 MUTATED SLC27A5 WILD-TYPE
  FEMALE               3               103
  MALE                 5               165
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC27A5 MUTATED       0                         0     8
  SLC27A5 WILD-TYPE     3                         1   264
D123V13, multiclass
                           clus
vv                          SLC27A5 MUTATED SLC27A5 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   8               264
[1] 3 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   3 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      0    7
  SLC27A5 WILD-TYPE    3  262
                        clus
vv                       SLC27A5 MUTATED SLC27A5 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               7               262
[1] 2 2
[1] FALSE

Clustering(124) Variable = PDE4DIP MUTATION ANALYSIS
D124V1, survival
                   sevent
clus2                 0   1
  PDE4DIP MUTATED    23  20
  PDE4DIP WILD-TYPE 103 120
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               43               223 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               20               120 
$`PDE4DIP MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51T 
        8.52        10.29        86.76        13.32        26.37        25.78 
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        62.79         1.08        39.62         9.99 
TCGA-EE-A29V TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MC TCGA-EE-A2MD 
        2.43        51.12        55.69         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        60.49       124.31       122.73        51.62         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 TCGA-RP-A693 
       28.73         0.99        44.28        84.72        10.13         0.33 
TCGA-RP-A694 
        0.69 

$`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        44.19         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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       31.30        54.31        32.28        21.44        32.61        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87        13.68        17.72        23.11        21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        13.22        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        8.12        12.20         5.13         4.31        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       15.85         9.21         1.18         7.99         9.90        11.15 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55        36.85         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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        34.29        17.98        60.00        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-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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       53.16        52.67         5.56        13.81        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 
       49.15        40.64         8.68         0.82         5.23         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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       11.61        31.33        16.24        15.42        12.16        14.70 
TCGA-QB-A6FS 
        5.79 

  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
             0.33              0.13 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
           124.31            125.65 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
            26.37             16.14 
[1] "0.3 - 124.3 (26.4)" "0.1 - 125.7 (16.1)"
[1] "hr=" "1.2"
D124V2, survival
                   sevent
clus2                 0   1
  PDE4DIP MUTATED    23  20
  PDE4DIP WILD-TYPE 106 121
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               43               227 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
               20               121 
$`PDE4DIP MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51T 
       16.67        43.43        86.76        60.23        39.75        26.89 
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        63.78         2.60        56.84        55.92 
TCGA-EE-A29V TCGA-EE-A2GB TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MC TCGA-EE-A2MD 
       25.87        59.28       126.81        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       134.40       124.31       122.73        51.62         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 TCGA-RP-A693 
       28.73        22.92       139.89        84.72        10.13         0.33 
TCGA-RP-A694 
        0.69 

$`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        62.07       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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       56.35       145.12        32.94        22.62        63.81       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29 
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       133.81       151.27        91.56       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        64.64 
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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       46.82       102.90        36.82        39.29        86.14        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       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       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       53.26        13.81        23.47       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       26.56        27.09        27.02        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-GF-A6C9 TCGA-GN-A264 
       19.30         9.90         7.23         2.04        11.74       117.93 
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 

  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
             0.33              0.16 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
           215.44            357.37 
  PDE4DIP MUTATED PDE4DIP WILD-TYPE 
            51.62             52.01 
[1] "0.3 - 215.4 (51.6)" "0.2 - 357.4 (52.0)"
[1] "hr=" "1"  
D124V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  PDE4DIP MUTATED                    7             1
  PDE4DIP WILD-TYPE                 32             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  PDE4DIP MUTATED                                           7
  PDE4DIP WILD-TYPE                                        53
                   vv
clus                REGIONAL LYMPH NODE
  PDE4DIP MUTATED                    29
  PDE4DIP WILD-TYPE                 142
D124V4, multiclass
                                           clus
vv                                          PDE4DIP MUTATED PDE4DIP WILD-TYPE
  DISTANT METASTASIS                                      7                32
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               7                53
  REGIONAL LYMPH NODE                                    29               142
[1] 4 2
[1] 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      22        9       21       11
                   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        24         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  PDE4DIP MUTATED            5          6        3
  PDE4DIP WILD-TYPE         18         40       13
D124V5, multiclass
             clus
vv            PDE4DIP MUTATED PDE4DIP WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   2                22
  STAGE IA                  1                 9
  STAGE IB                  3                21
  STAGE II                  5                11
  STAGE IIA                 1                 9
  STAGE IIB                 2                12
  STAGE IIC                 1                 8
  STAGE III                 8                24
  STAGE IIIA                2                11
  STAGE IIIB                5                18
  STAGE IIIC                6                40
  STAGE IV                  3                13
[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    42 50 44 49
D124V6, multiclass
       clus
vv      PDE4DIP MUTATED PDE4DIP WILD-TYPE
  T0+T1              10                42
  T2                  9                50
  T3                 10                44
  T4                  8                49
[1] 4 2
[1] TRUE
[1] "dimension of 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  10   7   3
  PDE4DIP WILD-TYPE 120  38  26  33
D124V7, multiclass
    clus
vv   PDE4DIP MUTATED PDE4DIP WILD-TYPE
  N0              19               120
  N1              10                38
  N2               7                26
  N3               3                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
  PDE4DIP MUTATED    38   0   0   0   3
  PDE4DIP WILD-TYPE 206   4   3   2   5
D124V8, multiclass
     clus
vv    PDE4DIP MUTATED PDE4DIP WILD-TYPE
  M0               38               206
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               3                 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"
D124V9, binary
                   cls
clus                 0  1
  PDE4DIP MUTATED   16 10
  PDE4DIP WILD-TYPE 87 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED     16   10
  PDE4DIP WILD-TYPE   87   58
     clus
vv    PDE4DIP MUTATED PDE4DIP WILD-TYPE
  NO               16                87
  YES              10                58
[1] 2 2
[1] FALSE
D124V10, binary
                   cls
clus                  0   1
  PDE4DIP MUTATED    10  34
  PDE4DIP WILD-TYPE  26 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED     10   34
  PDE4DIP WILD-TYPE   26  205
     clus
vv    PDE4DIP MUTATED PDE4DIP WILD-TYPE
  NO               10                26
  YES              34               205
[1] 2 2
[1] FALSE
D124V11, continuous
D124V12, binary
                   cls
clus                  0   1
  PDE4DIP MUTATED    16  28
  PDE4DIP WILD-TYPE  90 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED     16   28
  PDE4DIP WILD-TYPE   90  142
        clus
vv       PDE4DIP MUTATED PDE4DIP WILD-TYPE
  FEMALE              16                90
  MALE                28               142
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDE4DIP MUTATED       0                         0    44
  PDE4DIP WILD-TYPE     3                         1   228
D124V13, multiclass
                           clus
vv                          PDE4DIP MUTATED PDE4DIP WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  44               228
[1] 3 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  44
  PDE4DIP WILD-TYPE   3 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PDE4DIP MUTATED      0   44
  PDE4DIP WILD-TYPE    3  225
                        clus
vv                       PDE4DIP MUTATED PDE4DIP WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              44               225
[1] 2 2
[1] FALSE

Clustering(125) Variable = KANK3 MUTATION ANALYSIS
D125V1, survival
                 sevent
clus2               0   1
  KANK3 MUTATED     4   3
  KANK3 WILD-TYPE 122 137
  KANK3 MUTATED KANK3 WILD-TYPE 
              7             259 
  KANK3 MUTATED KANK3 WILD-TYPE 
              3             137 
$`KANK3 MUTATED`
TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3JI 
        9.99        36.30        28.31         9.53        60.49        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        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       125.65       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        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  KANK3 MUTATED KANK3 WILD-TYPE 
           0.99            0.13 
  KANK3 MUTATED KANK3 WILD-TYPE 
          60.49          125.65 
  KANK3 MUTATED KANK3 WILD-TYPE 
          28.31           16.47 
[1] "1.0 - 60.5 (28.3)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.3"
D125V2, survival
                 sevent
clus2               0   1
  KANK3 MUTATED     4   3
  KANK3 WILD-TYPE 125 138
  KANK3 MUTATED KANK3 WILD-TYPE 
              7             263 
  KANK3 MUTATED KANK3 WILD-TYPE 
              3             138 
$`KANK3 MUTATED`
TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3JI 
       35.93        36.82        75.48        47.28       134.40       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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        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        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       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       158.63       203.05       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       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  KANK3 MUTATED KANK3 WILD-TYPE 
          22.92            0.16 
  KANK3 MUTATED KANK3 WILD-TYPE 
         148.08          357.37 
  KANK3 MUTATED KANK3 WILD-TYPE 
          47.28           52.01 
[1] "22.9 - 148.1 (47.3)" "0.2 - 357.4 (52.0)" 
[1] "hr=" "1.2"
D125V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  KANK3 MUTATED                    1             0
  KANK3 WILD-TYPE                 38             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KANK3 MUTATED                                           2                   5
  KANK3 WILD-TYPE                                        58                 166
D125V4, multiclass
                                           clus
vv                                          KANK3 MUTATED KANK3 WILD-TYPE
  DISTANT METASTASIS                                    1              38
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   5             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
  KANK3 MUTATED             0       0       2        0        0        1
  KANK3 WILD-TYPE          10       6      22       10       24       15
                 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        31         13         23
                 vv
clus              STAGE IIIC STAGE IV
  KANK3 MUTATED            2        1
  KANK3 WILD-TYPE         44       15
D125V5, multiclass
             clus
vv            KANK3 MUTATED KANK3 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 2              22
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               1              31
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              2              44
  STAGE IV                1              15
[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    52 57 52 55
D125V6, multiclass
       clus
vv      KANK3 MUTATED KANK3 WILD-TYPE
  T0+T1             0              52
  T2                2              57
  T3                2              52
  T4                2              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
  KANK3 MUTATED     4   1   2   0
  KANK3 WILD-TYPE 135  47  31  36
D125V7, multiclass
    clus
vv   KANK3 MUTATED KANK3 WILD-TYPE
  N0             4             135
  N1             1              47
  N2             2              31
  N3             0              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               M0  M1 M1A M1B M1C
  KANK3 MUTATED     7   0   0   0   1
  KANK3 WILD-TYPE 237   4   3   2   7
D125V8, multiclass
     clus
vv    KANK3 MUTATED KANK3 WILD-TYPE
  M0              7             237
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             1               7
[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 101  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      2    4
  KANK3 WILD-TYPE  101   64
     clus
vv    KANK3 MUTATED KANK3 WILD-TYPE
  NO              2             101
  YES             4              64
[1] 2 2
[1] FALSE
D125V10, binary
                 cls
clus                0   1
  KANK3 MUTATED     0   8
  KANK3 WILD-TYPE  36 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      0    8
  KANK3 WILD-TYPE   36  231
     clus
vv    KANK3 MUTATED KANK3 WILD-TYPE
  NO              0              36
  YES             8             231
[1] 2 2
[1] FALSE
D125V11, continuous
D125V12, binary
                 cls
clus                0   1
  KANK3 MUTATED     1   7
  KANK3 WILD-TYPE 105 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      1    7
  KANK3 WILD-TYPE  105  163
        clus
vv       KANK3 MUTATED KANK3 WILD-TYPE
  FEMALE             1             105
  MALE               7             163
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KANK3 MUTATED       0                         0     8
  KANK3 WILD-TYPE     3                         1   264
D125V13, multiclass
                           clus
vv                          KANK3 MUTATED KANK3 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             264
[1] 3 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   8
  KANK3 WILD-TYPE   3 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK3 MUTATED      0    8
  KANK3 WILD-TYPE    3  261
                        clus
vv                       KANK3 MUTATED KANK3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             261
[1] 2 2
[1] FALSE

Clustering(126) Variable = RUNX1T1 MUTATION ANALYSIS
D126V1, survival
                   sevent
clus2                 0   1
  RUNX1T1 MUTATED    15  18
  RUNX1T1 WILD-TYPE 111 122
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               33               233 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               18               122 
$`RUNX1T1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A51T TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC 
       44.19        25.78        17.72         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 
       62.79         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 
       55.69         8.84        47.51         9.53        63.42        60.49 
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        86.76        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.28        21.44        32.61        52.01        47.87        13.68 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       23.11        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       13.35        11.57        10.55         6.31         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        60.23        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        7.99         9.90        36.85         1.08        39.62         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        32.15         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        47.21        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-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       98.27         2.70         6.18        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       125.65       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        53.16        52.67         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        52.08         8.65        49.15        40.64         8.68 
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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
             0.99              0.13 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
           124.31            125.65 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
            13.22             17.56 
[1] "1.0 - 124.3 (13.2)" "0.1 - 125.7 (17.6)"
[1] "hr=" "1.1"
D126V2, survival
                   sevent
clus2                 0   1
  RUNX1T1 MUTATED    15  18
  RUNX1T1 WILD-TYPE 114 123
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               33               237 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
               18               123 
$`RUNX1T1 MUTATED`
TCGA-D3-A2JF TCGA-D3-A51T TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC 
       62.07        26.89        18.18        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 
       63.78        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 
      126.81        21.67        61.51        47.28        96.23       134.40 
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        86.76        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.94        22.62        63.81       135.75       137.92       178.32 
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        22.29 
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        68.25        54.02        17.29        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 
      133.81        91.56       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 
       64.64         2.60        56.84        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       195.02        17.92       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28       314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21        53.26       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55       148.80        53.16        26.56        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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
            11.34              0.16 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
           151.27            357.37 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
            47.28             53.52 
[1] "11.3 - 151.3 (47.3)" "0.2 - 357.4 (53.5)" 
[1] "hr=" "1.4"
D126V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  RUNX1T1 MUTATED                    7             2
  RUNX1T1 WILD-TYPE                 32             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  RUNX1T1 MUTATED                                           6
  RUNX1T1 WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  RUNX1T1 MUTATED                    19
  RUNX1T1 WILD-TYPE                 152
D126V4, multiclass
                                           clus
vv                                          RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  DISTANT METASTASIS                                      7                32
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                54
  REGIONAL LYMPH NODE                                    19               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
  RUNX1T1 MUTATED             0       2       3        2        1        4
  RUNX1T1 WILD-TYPE          10       4      21        8       23       12
                   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        26         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  RUNX1T1 MUTATED            3          4        2
  RUNX1T1 WILD-TYPE         20         42       14
D126V5, multiclass
             clus
vv            RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   2                 4
  STAGE I                   3                21
  STAGE IA                  2                 8
  STAGE IB                  1                23
  STAGE II                  4                12
  STAGE IIA                 1                 9
  STAGE IIB                 3                11
  STAGE IIC                 1                 8
  STAGE III                 6                26
  STAGE IIIA                2                11
  STAGE IIIB                3                20
  STAGE IIIC                4                42
  STAGE IV                  2                14
[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    47 52 44 49
D126V6, multiclass
       clus
vv      RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  T0+T1               5                47
  T2                  7                52
  T3                 10                44
  T4                  8                49
[1] 4 2
[1] TRUE
[1] "dimension of 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   7   5   2
  RUNX1T1 WILD-TYPE 121  41  28  34
D126V7, multiclass
    clus
vv   RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  N0              18               121
  N1               7                41
  N2               5                28
  N3               2                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  RUNX1T1 MUTATED    32   0   0   0   2
  RUNX1T1 WILD-TYPE 212   4   3   2   6
D126V8, multiclass
     clus
vv    RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  M0               32               212
  M1                0                 4
  M1A               0                 3
  M1B               0                 2
  M1C               2                 6
[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 86 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED     17    8
  RUNX1T1 WILD-TYPE   86   60
     clus
vv    RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  NO               17                86
  YES               8                60
[1] 2 2
[1] FALSE
D126V10, binary
                   cls
clus                  0   1
  RUNX1T1 MUTATED     2  32
  RUNX1T1 WILD-TYPE  34 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      2   32
  RUNX1T1 WILD-TYPE   34  207
     clus
vv    RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  NO                2                34
  YES              32               207
[1] 2 2
[1] FALSE
D126V11, continuous
D126V12, binary
                   cls
clus                  0   1
  RUNX1T1 MUTATED     7  27
  RUNX1T1 WILD-TYPE  99 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      7   27
  RUNX1T1 WILD-TYPE   99  143
        clus
vv       RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  FEMALE               7                99
  MALE                27               143
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX1T1 MUTATED       0                         0    34
  RUNX1T1 WILD-TYPE     3                         1   238
D126V13, multiclass
                           clus
vv                          RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  34               238
[1] 3 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  34
  RUNX1T1 WILD-TYPE   3 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      0   34
  RUNX1T1 WILD-TYPE    3  235
                        clus
vv                       RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              34               235
[1] 2 2
[1] FALSE

Clustering(127) Variable = WDR12 MUTATION ANALYSIS
D127V1, survival
                 sevent
clus2               0   1
  WDR12 MUTATED     3   7
  WDR12 WILD-TYPE 123 133
  WDR12 MUTATED WDR12 WILD-TYPE 
             10             256 
  WDR12 MUTATED WDR12 WILD-TYPE 
              7             133 
$`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        86.76         1.08 
TCGA-EE-A2MI TCGA-EE-A3AB TCGA-ER-A19F TCGA-GN-A262 
       14.56       122.73        11.11        44.28 

$`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        44.19         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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87        13.68        17.72        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        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 
       60.23         4.34        15.85         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        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
        9.53        29.46         2.73        44.25         7.96        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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 
       60.49        53.16        52.67         5.56       124.31        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  WDR12 MUTATED WDR12 WILD-TYPE 
           1.08            0.13 
  WDR12 MUTATED WDR12 WILD-TYPE 
         122.73          125.65 
  WDR12 MUTATED WDR12 WILD-TYPE 
         12.835          17.445 
[1] "1.1 - 122.7 (12.8)" "0.1 - 125.7 (17.4)"
[1] "hr=" "1.2"
D127V2, survival
                 sevent
clus2               0   1
  WDR12 MUTATED     4   7
  WDR12 WILD-TYPE 125 134
  WDR12 MUTATED WDR12 WILD-TYPE 
             11             259 
  WDR12 MUTATED WDR12 WILD-TYPE 
              7             134 
$`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        86.76       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       139.89 

$`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        62.07       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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 
      135.75       137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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 
       63.78        72.07        64.64        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96        96.23       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       124.31        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23         2.04        11.74       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  WDR12 MUTATED WDR12 WILD-TYPE 
           2.60            0.16 
  WDR12 MUTATED WDR12 WILD-TYPE 
         204.66          357.37 
  WDR12 MUTATED WDR12 WILD-TYPE 
          71.80           51.35 
[1] "2.6 - 204.7 (71.8)" "0.2 - 357.4 (51.4)"
[1] "hr=" "1.1"
D127V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  WDR12 MUTATED                    0             0
  WDR12 WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  WDR12 MUTATED                                           2                   9
  WDR12 WILD-TYPE                                        58                 162
D127V4, multiclass
                                           clus
vv                                          WDR12 MUTATED WDR12 WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   9             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
  WDR12 MUTATED             0       0       0        0        1        0
  WDR12 WILD-TYPE          10       6      24       10       23       16
                 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        29         13         23
                 vv
clus              STAGE IIIC STAGE IV
  WDR12 MUTATED            1        0
  WDR12 WILD-TYPE         45       16
D127V5, multiclass
             clus
vv            WDR12 MUTATED WDR12 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               2              12
  STAGE IIC               1               8
  STAGE III               3              29
  STAGE IIIA              0              13
  STAGE IIIB              0              23
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    50 58 53 53
D127V6, multiclass
       clus
vv      WDR12 MUTATED WDR12 WILD-TYPE
  T0+T1             2              50
  T2                1              58
  T3                1              53
  T4                4              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
  WDR12 MUTATED     5   1   2   2
  WDR12 WILD-TYPE 134  47  31  34
D127V7, multiclass
    clus
vv   WDR12 MUTATED WDR12 WILD-TYPE
  N0             5             134
  N1             1              47
  N2             2              31
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  WDR12 MUTATED     9   0   0   1   0
  WDR12 WILD-TYPE 235   4   3   1   8
D127V8, multiclass
     clus
vv    WDR12 MUTATED WDR12 WILD-TYPE
  M0              9             235
  M1              0               4
  M1A             0               3
  M1B             1               1
  M1C             0               8
[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 101  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      2    3
  WDR12 WILD-TYPE  101   65
     clus
vv    WDR12 MUTATED WDR12 WILD-TYPE
  NO              2             101
  YES             3              65
[1] 2 2
[1] FALSE
D127V10, binary
                 cls
clus                0   1
  WDR12 MUTATED     2   9
  WDR12 WILD-TYPE  34 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      2    9
  WDR12 WILD-TYPE   34  230
     clus
vv    WDR12 MUTATED WDR12 WILD-TYPE
  NO              2              34
  YES             9             230
[1] 2 2
[1] FALSE
D127V11, continuous
D127V12, binary
                 cls
clus                0   1
  WDR12 MUTATED     2   9
  WDR12 WILD-TYPE 104 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      2    9
  WDR12 WILD-TYPE  104  161
        clus
vv       WDR12 MUTATED WDR12 WILD-TYPE
  FEMALE             2             104
  MALE               9             161
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR12 MUTATED       0                         0    11
  WDR12 WILD-TYPE     3                         1   261
D127V13, multiclass
                           clus
vv                          WDR12 MUTATED WDR12 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             261
[1] 3 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   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR12 MUTATED      0   11
  WDR12 WILD-TYPE    3  258
                        clus
vv                       WDR12 MUTATED WDR12 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             258
[1] 2 2
[1] FALSE

Clustering(128) Variable = POTEG MUTATION ANALYSIS
D128V1, survival
                 sevent
clus2               0   1
  POTEG MUTATED    14  16
  POTEG WILD-TYPE 112 124
  POTEG MUTATED POTEG WILD-TYPE 
             30             236 
  POTEG MUTATED POTEG WILD-TYPE 
             16             124 
$`POTEG MUTATED`
TCGA-D3-A2JF TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A182 
       44.19         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        39.62         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 TCGA-RP-A694 
       40.64         5.23        53.85         6.41         0.99         0.69 

$`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        86.76        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
       13.68        17.72        23.11         4.01        21.93        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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        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        60.23 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       15.85         1.18         7.99         9.90        37.97        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55        36.85         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-A2A6 
       32.15         8.09        11.31        49.22        36.30        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       51.12        34.29        17.98        60.00        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        55.69         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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       44.25         7.96       125.65       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        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31        51.62         3.68        30.15        13.81        15.95 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
        3.22        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.11       114.15        34.88        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       12.89        47.38         8.65         8.81        49.15         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.39         0.82         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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 
        5.79         0.33 

  POTEG MUTATED POTEG WILD-TYPE 
           0.69            0.13 
  POTEG MUTATED POTEG WILD-TYPE 
         122.73          125.65 
  POTEG MUTATED POTEG WILD-TYPE 
         11.935          17.720 
[1] "0.7 - 122.7 (11.9)" "0.1 - 125.7 (17.7)"
[1] "hr=" "1.2"
D128V2, survival
                 sevent
clus2               0   1
  POTEG MUTATED    14  16
  POTEG WILD-TYPE 115 125
  POTEG MUTATED POTEG WILD-TYPE 
             30             240 
  POTEG MUTATED POTEG WILD-TYPE 
             16             125 
$`POTEG MUTATED`
TCGA-D3-A2JF TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A182 
       62.07         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        56.84        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 TCGA-RP-A694 
       53.16        27.02        77.82        49.45        22.92         0.69 

$`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        86.76        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29        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        68.25        54.02        17.29 
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       133.81        91.56        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        63.78        72.07        64.64 
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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       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 
      134.40       162.48        71.21        53.26       124.31        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
        3.68        54.51        13.81        23.47       172.18        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 

  POTEG MUTATED POTEG WILD-TYPE 
           0.69            0.16 
  POTEG MUTATED POTEG WILD-TYPE 
         204.66          357.37 
  POTEG MUTATED POTEG WILD-TYPE 
         54.540          51.485 
[1] "0.7 - 204.7 (54.5)" "0.2 - 357.4 (51.5)"
[1] "hr=" "1.1"
D128V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  POTEG MUTATED                    9             2
  POTEG WILD-TYPE                 30             3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  POTEG MUTATED                                           6                  14
  POTEG WILD-TYPE                                        54                 157
D128V4, multiclass
                                           clus
vv                                          POTEG MUTATED POTEG WILD-TYPE
  DISTANT METASTASIS                                    9              30
  PRIMARY TUMOR                                         2               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             6              54
  REGIONAL LYMPH NODE                                  14             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
  POTEG MUTATED             0       1       2        2        3        3
  POTEG WILD-TYPE          10       5      22        8       21       13
                 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        28         11         22
                 vv
clus              STAGE IIIC STAGE IV
  POTEG MUTATED            5        3
  POTEG WILD-TYPE         41       13
D128V5, multiclass
             clus
vv            POTEG MUTATED POTEG WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 2              22
  STAGE IA                2               8
  STAGE IB                3              21
  STAGE II                3              13
  STAGE IIA               2               8
  STAGE IIB               3              11
  STAGE IIC               0               9
  STAGE III               4              28
  STAGE IIIA              2              11
  STAGE IIIB              1              22
  STAGE IIIC              5              41
  STAGE IV                3              13
[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    48 52 44 52
D128V6, multiclass
       clus
vv      POTEG MUTATED POTEG WILD-TYPE
  T0+T1             4              48
  T2                7              52
  T3               10              44
  T4                5              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
  POTEG MUTATED    17   6   3   3
  POTEG WILD-TYPE 122  42  30  33
D128V7, multiclass
    clus
vv   POTEG MUTATED POTEG WILD-TYPE
  N0            17             122
  N1             6              42
  N2             3              30
  N3             3              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
  POTEG MUTATED    28   1   0   0   2
  POTEG WILD-TYPE 216   3   3   2   6
D128V8, multiclass
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  M0             28             216
  M1              1               3
  M1A             0               3
  M1B             0               2
  M1C             2               6
[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 91 60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED     12    8
  POTEG WILD-TYPE   91   60
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  NO             12              91
  YES             8              60
[1] 2 2
[1] FALSE
D128V10, binary
                 cls
clus                0   1
  POTEG MUTATED     4  27
  POTEG WILD-TYPE  32 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      4   27
  POTEG WILD-TYPE   32  212
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  NO              4              32
  YES            27             212
[1] 2 2
[1] FALSE
D128V11, continuous
D128V12, binary
                 cls
clus                0   1
  POTEG MUTATED     9  22
  POTEG WILD-TYPE  97 148
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      9   22
  POTEG WILD-TYPE   97  148
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  FEMALE             9              97
  MALE              22             148
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POTEG MUTATED       0                         0    31
  POTEG WILD-TYPE     3                         1   241
D128V13, multiclass
                           clus
vv                          POTEG MUTATED POTEG WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                31             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"
D128V14, binary
                 cls
clus                0   1
  POTEG MUTATED     1  30
  POTEG WILD-TYPE   2 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      1   30
  POTEG WILD-TYPE    2  239
                        clus
vv                       POTEG MUTATED POTEG WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            30             239
[1] 2 2
[1] FALSE

Clustering(129) Variable = ITPR2 MUTATION ANALYSIS
D129V1, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED    10   6
  ITPR2 WILD-TYPE 116 134
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             16             250 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              6             134 
$`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-A3JB 
       49.22         9.53       111.91        21.60        21.60         0.95 
TCGA-EE-A3JD TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GF-A4EO 
       27.35        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.35        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        60.23        15.85         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        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43        32.15         8.09        11.31        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        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 
       55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        22.22        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       14.20         5.98         6.41         2.27         0.20         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        0.16        17.33         9.90         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
           0.95            0.13 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         111.91          125.65 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         14.025          17.445 
[1] "0.9 - 111.9 (14.0)" "0.1 - 125.7 (17.4)"
[1] "hr=" "1.3"
D129V2, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED    10   6
  ITPR2 WILD-TYPE 119 135
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             16             254 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              6             135 
$`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-A3JB 
      102.90        47.28       203.05        36.95        64.08       201.80 
TCGA-EE-A3JD TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GF-A4EO 
       27.35        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       17.29        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       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       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 
       63.78        72.07        64.64         2.60        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       28.83        19.76        61.51       103.27       268.73       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       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88         0.20        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
           7.23            0.16 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         203.05          357.37 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         47.130          53.175 
[1] "7.2 - 203.1 (47.1)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.3"
D129V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ITPR2 MUTATED                    1             1
  ITPR2 WILD-TYPE                 38             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ITPR2 MUTATED                                           3                  11
  ITPR2 WILD-TYPE                                        57                 160
D129V4, multiclass
                                           clus
vv                                          ITPR2 MUTATED ITPR2 WILD-TYPE
  DISTANT METASTASIS                                    1              38
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             3              57
  REGIONAL LYMPH NODE                                  11             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
  ITPR2 MUTATED             0       1       1        0        1        2
  ITPR2 WILD-TYPE          10       5      23       10       23       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ITPR2 MUTATED           0         0         0         5          1          2
  ITPR2 WILD-TYPE        10        14         9        27         12         21
                 vv
clus              STAGE IIIC STAGE IV
  ITPR2 MUTATED            3        0
  ITPR2 WILD-TYPE         43       16
D129V5, multiclass
             clus
vv            ITPR2 MUTATED ITPR2 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 1              23
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              14
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               5              27
  STAGE IIIA              1              12
  STAGE IIIB              2              21
  STAGE IIIC              3              43
  STAGE IV                0              16
[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       3  3  5  2
  ITPR2 WILD-TYPE    49 56 49 55
D129V6, multiclass
       clus
vv      ITPR2 MUTATED ITPR2 WILD-TYPE
  T0+T1             3              49
  T2                3              56
  T3                5              49
  T4                2              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
  ITPR2 MUTATED     5   5   4   2
  ITPR2 WILD-TYPE 134  43  29  34
D129V7, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  N0             5             134
  N1             5              43
  N2             4              29
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  ITPR2 MUTATED    16   0   0   0   0
  ITPR2 WILD-TYPE 228   4   3   2   8
D129V8, multiclass
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  M0             16             228
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 98 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      5    4
  ITPR2 WILD-TYPE   98   64
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO              5              98
  YES             4              64
[1] 2 2
[1] FALSE
D129V10, binary
                 cls
clus                0   1
  ITPR2 MUTATED     4  12
  ITPR2 WILD-TYPE  32 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      4   12
  ITPR2 WILD-TYPE   32  227
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO              4              32
  YES            12             227
[1] 2 2
[1] FALSE
D129V11, continuous
D129V12, binary
                 cls
clus                0   1
  ITPR2 MUTATED     5  11
  ITPR2 WILD-TYPE 101 159
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      5   11
  ITPR2 WILD-TYPE  101  159
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  FEMALE             5             101
  MALE              11             159
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITPR2 MUTATED       0                         0    16
  ITPR2 WILD-TYPE     3                         1   256
D129V13, multiclass
                           clus
vv                          ITPR2 MUTATED ITPR2 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                16             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"
D129V14, binary
                 cls
clus                0   1
  ITPR2 MUTATED     0  16
  ITPR2 WILD-TYPE   3 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      0   16
  ITPR2 WILD-TYPE    3  253
                        clus
vv                       ITPR2 MUTATED ITPR2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            16             253
[1] 2 2
[1] FALSE

Clustering(130) Variable = CRNKL1 MUTATION ANALYSIS
D130V1, survival
                  sevent
clus2                0   1
  CRNKL1 MUTATED     7   5
  CRNKL1 WILD-TYPE 119 135
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              12              254 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
               5              135 
$`CRNKL1 MUTATED`
TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A2GB TCGA-EE-A2GU 
       54.31        13.22         1.35         4.34        51.12        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        53.16        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       34.98         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73        44.25         7.96        63.42       125.65       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        60.49        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
        5.56       124.31       122.73        51.62         3.68        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22         0.95        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
            1.35             0.13 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
           98.27           125.65 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
          28.750           16.355 
[1] "1.4 - 98.3 (28.8)"  "0.1 - 125.7 (16.4)"
[1] "hr=" "1.5"
D130V2, survival
                  sevent
clus2                0   1
  CRNKL1 MUTATED     7   5
  CRNKL1 WILD-TYPE 122 136
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
              12              258 
  CRNKL1 MUTATED CRNKL1 WILD-TYPE 
               5              136 
$`CRNKL1 MUTATED`
TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A2GB TCGA-EE-A2GU 
      145.12        66.25        14.70       151.27        59.28        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       162.48        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        67.43       314.56       161.03       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 
      126.81        13.91        14.30        55.59        44.88        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96        96.23       158.63       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       134.40        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  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           50.825 
[1] "14.7 - 204.7 (80.5)" "0.2 - 357.4 (50.8)" 
[1] "hr=" "1.6"
D130V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CRNKL1 MUTATED                    3             1
  CRNKL1 WILD-TYPE                 36             4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CRNKL1 MUTATED                                           1
  CRNKL1 WILD-TYPE                                        59
                  vv
clus               REGIONAL LYMPH NODE
  CRNKL1 MUTATED                     8
  CRNKL1 WILD-TYPE                 163
D130V4, multiclass
                                           clus
vv                                          CRNKL1 MUTATED CRNKL1 WILD-TYPE
  DISTANT METASTASIS                                     3               36
  PRIMARY TUMOR                                          1                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              1               59
  REGIONAL LYMPH NODE                                    8              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
  CRNKL1 MUTATED             0       1       2        2        0        1
  CRNKL1 WILD-TYPE          10       5      22        8       24       15
                  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        30         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CRNKL1 MUTATED            1          1        1
  CRNKL1 WILD-TYPE         22         45       15
D130V5, multiclass
             clus
vv            CRNKL1 MUTATED CRNKL1 WILD-TYPE
  I OR II NOS              0               10
  STAGE 0                  1                5
  STAGE I                  2               22
  STAGE IA                 2                8
  STAGE IB                 0               24
  STAGE II                 1               15
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                0                9
  STAGE III                2               30
  STAGE IIIA               1               12
  STAGE IIIB               1               22
  STAGE IIIC               1               45
  STAGE IV                 1               15
[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    48 57 52 55
D130V6, multiclass
       clus
vv      CRNKL1 MUTATED CRNKL1 WILD-TYPE
  T0+T1              4               48
  T2                 2               57
  T3                 2               52
  T4                 2               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
  CRNKL1 MUTATED     7   4   1   0
  CRNKL1 WILD-TYPE 132  44  32  36
D130V7, multiclass
    clus
vv   CRNKL1 MUTATED CRNKL1 WILD-TYPE
  N0              7              132
  N1              4               44
  N2              1               32
  N3              0               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                M0  M1 M1A M1B M1C
  CRNKL1 MUTATED    12   0   0   0   1
  CRNKL1 WILD-TYPE 232   4   3   2   7
D130V8, multiclass
     clus
vv    CRNKL1 MUTATED CRNKL1 WILD-TYPE
  M0              12              232
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              1                7
[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 97 66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      6    2
  CRNKL1 WILD-TYPE   97   66
     clus
vv    CRNKL1 MUTATED CRNKL1 WILD-TYPE
  NO               6               97
  YES              2               66
[1] 2 2
[1] FALSE
D130V10, binary
                  cls
clus                 0   1
  CRNKL1 MUTATED     2  11
  CRNKL1 WILD-TYPE  34 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      2   11
  CRNKL1 WILD-TYPE   34  228
     clus
vv    CRNKL1 MUTATED CRNKL1 WILD-TYPE
  NO               2               34
  YES             11              228
[1] 2 2
[1] FALSE
D130V11, continuous
D130V12, binary
                  cls
clus                 0   1
  CRNKL1 MUTATED     4   9
  CRNKL1 WILD-TYPE 102 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      4    9
  CRNKL1 WILD-TYPE  102  161
        clus
vv       CRNKL1 MUTATED CRNKL1 WILD-TYPE
  FEMALE              4              102
  MALE                9              161
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRNKL1 MUTATED       0                         0    13
  CRNKL1 WILD-TYPE     3                         1   259
D130V13, multiclass
                           clus
vv                          CRNKL1 MUTATED CRNKL1 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 13              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"
D130V14, binary
                  cls
clus                 0   1
  CRNKL1 MUTATED     0  13
  CRNKL1 WILD-TYPE   3 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRNKL1 MUTATED      0   13
  CRNKL1 WILD-TYPE    3  256
                        clus
vv                       CRNKL1 MUTATED CRNKL1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             13              256
[1] 2 2
[1] FALSE

Clustering(131) Variable = DSP MUTATION ANALYSIS
D131V1, survival
               sevent
clus2             0   1
  DSP MUTATED    25  32
  DSP WILD-TYPE 101 108
  DSP MUTATED DSP WILD-TYPE 
           57           209 
  DSP MUTATED DSP WILD-TYPE 
           32           108 
$`DSP MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3ML TCGA-D3-A51T 
        8.38        11.41        44.19        36.16         6.31        25.78 
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        62.79         1.08        39.62         9.50 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M5 
       36.30        34.29        30.08        35.54         5.42         8.84 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
        9.53         2.73        63.42        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J8 
       53.16        51.62        30.15        13.81        15.95        16.14 
TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19W TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       22.22        31.40        17.72        15.72        23.80        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZZ TCGA-FS-A4FC 
        7.30        12.89         8.65         8.81         5.23         6.41 
TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A267 
        0.99        11.61        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        86.76         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        59.57       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        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       31.30        54.31        32.28        21.44        32.61        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A184 
       13.35        13.22        10.55         6.31         8.12         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31        60.23        15.85         1.18         7.99         9.90 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        8.55        36.85        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        32.15         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 
       36.33        51.12        17.98        60.00        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        28.31        33.83        55.69         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-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       56.02        25.08        52.67         5.56       124.31       122.73 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
        0.95        27.35        18.41        21.73        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-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        5.62        18.41        85.74        64.47         3.45        11.01 
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-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        47.38        52.08 
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-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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        0.85        44.28        31.33        84.72        10.13        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  DSP MUTATED DSP WILD-TYPE 
         0.99          0.13 
  DSP MUTATED DSP WILD-TYPE 
        63.42        125.65 
  DSP MUTATED DSP WILD-TYPE 
        15.72         17.98 
[1] "1.0 - 63.4 (15.7)"  "0.1 - 125.7 (18.0)"
[1] "hr=" "1.2"
D131V2, survival
               sevent
clus2             0   1
  DSP MUTATED    25  32
  DSP WILD-TYPE 104 109
  DSP MUTATED DSP WILD-TYPE 
           57           213 
  DSP MUTATED DSP WILD-TYPE 
           32           109 
$`DSP MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3ML TCGA-D3-A51T 
       65.49        11.87        62.07        42.08        13.87        26.89 
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        63.78         2.60        56.84        18.61 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M5 
       36.82        67.43        48.72        79.66        13.91        21.67 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       47.28       268.73        96.23       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J8 
      162.48        51.62        54.51        13.81        23.47        34.32 
TCGA-EE-A3JA TCGA-ER-A193 TCGA-ER-A19W TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       53.19        31.40       148.18        15.72       202.65        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZZ TCGA-FS-A4FC 
       27.72        23.93       133.55        11.41        27.02        49.45 
TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A267 
       22.92        11.74        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        86.76       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        59.57       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        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
       56.35       145.12        32.94        22.62        63.81       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
       91.56        13.55        63.35        80.61        72.07        64.64 
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       195.02 
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        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM 
      314.56       161.03       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       126.81        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       158.63       203.05       167.90        47.54 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH 
       71.21        53.26       124.31       122.73         3.68       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        36.95        64.08       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58       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-A19T TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25         8.88        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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      174.21       216.92        48.59       228.59        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-A1ZS TCGA-FS-A1ZT 
       32.75        47.38       101.26        74.73       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-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        19.30         9.90         7.23         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        10.13        62.79        32.48        39.58 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  DSP MUTATED DSP WILD-TYPE 
         2.60          0.16 
  DSP MUTATED DSP WILD-TYPE 
       268.73        357.37 
  DSP MUTATED DSP WILD-TYPE 
        47.28         54.02 
[1] "2.6 - 268.7 (47.3)" "0.2 - 357.4 (54.0)"
[1] "hr=" "1.2"
D131V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  DSP MUTATED                   13             1
  DSP WILD-TYPE                 26             4
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DSP MUTATED                                           9                  36
  DSP WILD-TYPE                                        51                 135
D131V4, multiclass
                                           clus
vv                                          DSP MUTATED DSP WILD-TYPE
  DISTANT METASTASIS                                 13            26
  PRIMARY TUMOR                                       1             4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           9            51
  REGIONAL LYMPH NODE                                36           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       5        5        5        5
  DSP WILD-TYPE           8       3      19        5       19       11
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DSP MUTATED           2         3         0         4          5          6
  DSP WILD-TYPE         8        11         9        28          8         17
               vv
clus            STAGE IIIC STAGE IV
  DSP MUTATED           10        3
  DSP WILD-TYPE         36       13
D131V5, multiclass
             clus
vv            DSP MUTATED DSP WILD-TYPE
  I OR II NOS           2             8
  STAGE 0               3             3
  STAGE I               5            19
  STAGE IA              5             5
  STAGE IB              5            19
  STAGE II              5            11
  STAGE IIA             2             8
  STAGE IIB             3            11
  STAGE IIC             0             9
  STAGE III             4            28
  STAGE IIIA            5             8
  STAGE IIIB            6            17
  STAGE IIIC           10            36
  STAGE IV              3            13
[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 12 13 11
  DSP WILD-TYPE    40 47 41 46
D131V6, multiclass
       clus
vv      DSP MUTATED DSP WILD-TYPE
  T0+T1          12            40
  T2             12            47
  T3             13            41
  T4             11            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
  DSP MUTATED    33  10   8   5
  DSP WILD-TYPE 106  38  25  31
D131V7, multiclass
    clus
vv   DSP MUTATED DSP WILD-TYPE
  N0          33           106
  N1          10            38
  N2           8            25
  N3           5            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
  DSP MUTATED    53   1   0   0   2
  DSP WILD-TYPE 191   3   3   2   6
D131V8, multiclass
     clus
vv    DSP MUTATED DSP WILD-TYPE
  M0           53           191
  M1            1             3
  M1A           0             3
  M1B           0             2
  M1C           2             6
[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 77 56
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     26   12
  DSP WILD-TYPE   77   56
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO           26            77
  YES          12            56
[1] 2 2
[1] FALSE
D131V10, binary
               cls
clus              0   1
  DSP MUTATED     8  51
  DSP WILD-TYPE  28 188
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      8   51
  DSP WILD-TYPE   28  188
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO            8            28
  YES          51           188
[1] 2 2
[1] FALSE
D131V11, continuous
D131V12, binary
               cls
clus              0   1
  DSP MUTATED    20  39
  DSP WILD-TYPE  86 131
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     20   39
  DSP WILD-TYPE   86  131
        clus
vv       DSP MUTATED DSP WILD-TYPE
  FEMALE          20            86
  MALE            39           131
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSP MUTATED       0                         0    59
  DSP WILD-TYPE     3                         1   213
D131V13, multiclass
                           clus
vv                          DSP MUTATED DSP WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              59           213
[1] 3 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  57
  DSP WILD-TYPE   2 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      1   57
  DSP WILD-TYPE    2  212
                        clus
vv                       DSP MUTATED DSP WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          57           212
[1] 2 2
[1] FALSE

Clustering(132) Variable = SF3B1 MUTATION ANALYSIS
D132V1, survival
                 sevent
clus2               0   1
  SF3B1 MUTATED     7   6
  SF3B1 WILD-TYPE 119 134
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             253 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
              6             134 
$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56       125.65       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        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T 
       13.45        28.60        42.84        34.68         9.57         6.58 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       17.72        78.44        11.80         1.87         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A 
       11.74         6.58        22.49         1.71         5.62        85.74 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72        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-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        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
           1.08            0.13 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          92.42          125.65 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          18.41           16.47 
[1] "1.1 - 92.4 (18.4)"  "0.1 - 125.7 (16.5)"
[1] "hr=" "1.2"
D132V2, survival
                 sevent
clus2               0   1
  SF3B1 MUTATED     7   6
  SF3B1 WILD-TYPE 122 135
  SF3B1 MUTATED SF3B1 WILD-TYPE 
             13             257 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
              6             135 
$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64        56.84 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
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       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-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-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET 
       43.82        23.34        20.15        31.27        32.05        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       46.98        33.21         6.77       174.21        15.72       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-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-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  SF3B1 MUTATED SF3B1 WILD-TYPE 
           2.60            0.16 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
         247.04          357.37 
  SF3B1 MUTATED SF3B1 WILD-TYPE 
          37.25           53.16 
[1] "2.6 - 247.0 (37.2)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.1"
D132V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  SF3B1 MUTATED                    1             1
  SF3B1 WILD-TYPE                 38             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  SF3B1 MUTATED                                           1                  10
  SF3B1 WILD-TYPE                                        59                 161
D132V4, multiclass
                                           clus
vv                                          SF3B1 MUTATED SF3B1 WILD-TYPE
  DISTANT METASTASIS                                    1              38
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                  10             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
  SF3B1 MUTATED             1       0       0        1        2        1
  SF3B1 WILD-TYPE           9       6      24        9       22       15
                 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        31         13         21
                 vv
clus              STAGE IIIC STAGE IV
  SF3B1 MUTATED            2        0
  SF3B1 WILD-TYPE         44       16
D132V5, multiclass
             clus
vv            SF3B1 MUTATED SF3B1 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                1               9
  STAGE IB                2              22
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               1              31
  STAGE IIIA              0              13
  STAGE IIIB              2              21
  STAGE IIIC              2              44
  STAGE IV                0              16
[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    50 56 53 54
D132V6, multiclass
       clus
vv      SF3B1 MUTATED SF3B1 WILD-TYPE
  T0+T1             2              50
  T2                3              56
  T3                1              53
  T4                3              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
  SF3B1 MUTATED     7   0   2   2
  SF3B1 WILD-TYPE 132  48  31  34
D132V7, multiclass
    clus
vv   SF3B1 MUTATED SF3B1 WILD-TYPE
  N0             7             132
  N1             0              48
  N2             2              31
  N3             2              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  SF3B1 MUTATED    11   0   0   0   0
  SF3B1 WILD-TYPE 233   4   3   2   8
D132V8, multiclass
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  M0             11             233
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 98 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      5    2
  SF3B1 WILD-TYPE   98   66
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  NO              5              98
  YES             2              66
[1] 2 2
[1] FALSE
D132V10, binary
                 cls
clus                0   1
  SF3B1 MUTATED     2  11
  SF3B1 WILD-TYPE  34 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      2   11
  SF3B1 WILD-TYPE   34  228
     clus
vv    SF3B1 MUTATED SF3B1 WILD-TYPE
  NO              2              34
  YES            11             228
[1] 2 2
[1] FALSE
D132V11, continuous
D132V12, binary
                 cls
clus                0   1
  SF3B1 MUTATED     6   7
  SF3B1 WILD-TYPE 100 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      6    7
  SF3B1 WILD-TYPE  100  163
        clus
vv       SF3B1 MUTATED SF3B1 WILD-TYPE
  FEMALE             6             100
  MALE               7             163
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SF3B1 MUTATED       0                         0    13
  SF3B1 WILD-TYPE     3                         1   259
D132V13, multiclass
                           clus
vv                          SF3B1 MUTATED SF3B1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             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"
D132V14, binary
                 cls
clus                0   1
  SF3B1 MUTATED     0  13
  SF3B1 WILD-TYPE   3 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B1 MUTATED      0   13
  SF3B1 WILD-TYPE    3  256
                        clus
vv                       SF3B1 MUTATED SF3B1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             256
[1] 2 2
[1] FALSE

Clustering(133) Variable = CAGE1 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  CAGE1 MUTATED     5   6
  CAGE1 WILD-TYPE 121 134
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             255 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
              6             134 
$`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        36.33 
TCGA-EE-A2GI TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-FS-A1ZK TCGA-FW-A3R5 
       30.08         8.84        53.16        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31        60.23        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        51.12        34.29        17.98        60.00 
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 
       55.69         5.42         1.15        13.02        34.98        36.33 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        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-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  CAGE1 MUTATED CAGE1 WILD-TYPE 
           0.99            0.13 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
          53.16          125.65 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
           9.99           17.72 
[1] "1.0 - 53.2 (10.0)"  "0.1 - 125.7 (17.7)"
[1] "hr=" "1.5"
D133V2, survival
                 sevent
clus2               0   1
  CAGE1 MUTATED     5   6
  CAGE1 WILD-TYPE 124 135
  CAGE1 MUTATED CAGE1 WILD-TYPE 
             11             259 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
              6             135 
$`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        86.14 
TCGA-EE-A2GI TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-FS-A1ZK TCGA-FW-A3R5 
       48.72        21.67       162.48        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       56.84        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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       59.28        67.43       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       134.40        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  CAGE1 MUTATED CAGE1 WILD-TYPE 
          21.67            0.16 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
         162.48          357.37 
  CAGE1 MUTATED CAGE1 WILD-TYPE 
          48.72           52.01 
[1] "21.7 - 162.5 (48.7)" "0.2 - 357.4 (52.0)" 
[1] "hr=" "1.2"
D133V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CAGE1 MUTATED                    2             1
  CAGE1 WILD-TYPE                 37             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CAGE1 MUTATED                                           1                   7
  CAGE1 WILD-TYPE                                        59                 164
D133V4, multiclass
                                           clus
vv                                          CAGE1 MUTATED CAGE1 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             1              59
  REGIONAL LYMPH NODE                                   7             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
  CAGE1 MUTATED             0       1       1        2        0        3
  CAGE1 WILD-TYPE          10       5      23        8       24       13
                 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        31         12         23
                 vv
clus              STAGE IIIC STAGE IV
  CAGE1 MUTATED            1        0
  CAGE1 WILD-TYPE         45       16
D133V5, multiclass
             clus
vv            CAGE1 MUTATED CAGE1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 1              23
  STAGE IA                2               8
  STAGE IB                0              24
  STAGE II                3              13
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               1              31
  STAGE IIIA              1              12
  STAGE IIIB              0              23
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    50 58 49 56
D133V6, multiclass
       clus
vv      CAGE1 MUTATED CAGE1 WILD-TYPE
  T0+T1             2              50
  T2                1              58
  T3                5              49
  T4                1              56
[1] 4 2
[1] TRUE
[1] "dimension of 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 131  47  31  36
D133V7, multiclass
    clus
vv   CAGE1 MUTATED CAGE1 WILD-TYPE
  N0             8             131
  N1             1              47
  N2             2              31
  N3             0              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               M0  M1 M1A M1B M1C
  CAGE1 MUTATED    11   0   0   0   0
  CAGE1 WILD-TYPE 233   4   3   2   8
D133V8, multiclass
     clus
vv    CAGE1 MUTATED CAGE1 WILD-TYPE
  M0             11             233
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 97 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      6    1
  CAGE1 WILD-TYPE   97   67
     clus
vv    CAGE1 MUTATED CAGE1 WILD-TYPE
  NO              6              97
  YES             1              67
[1] 2 2
[1] FALSE
D133V10, binary
                 cls
clus                0   1
  CAGE1 MUTATED     0  11
  CAGE1 WILD-TYPE  36 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      0   11
  CAGE1 WILD-TYPE   36  228
     clus
vv    CAGE1 MUTATED CAGE1 WILD-TYPE
  NO              0              36
  YES            11             228
[1] 2 2
[1] FALSE
D133V11, continuous
D133V12, binary
                 cls
clus                0   1
  CAGE1 MUTATED     2   9
  CAGE1 WILD-TYPE 104 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      2    9
  CAGE1 WILD-TYPE  104  161
        clus
vv       CAGE1 MUTATED CAGE1 WILD-TYPE
  FEMALE             2             104
  MALE               9             161
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CAGE1 MUTATED       0                         0    11
  CAGE1 WILD-TYPE     3                         1   261
D133V13, multiclass
                           clus
vv                          CAGE1 MUTATED CAGE1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             261
[1] 3 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   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAGE1 MUTATED      0   11
  CAGE1 WILD-TYPE    3  258
                        clus
vv                       CAGE1 MUTATED CAGE1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             258
[1] 2 2
[1] FALSE

Clustering(134) Variable = DDX43 MUTATION ANALYSIS
D134V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     4   6
  DDX43 WILD-TYPE 122 134
  DDX43 MUTATED DDX43 WILD-TYPE 
             10             256 
  DDX43 MUTATED DDX43 WILD-TYPE 
              6             134 
$`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        60.49        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        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       125.65       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        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22         0.95        18.41        21.73        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-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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       10.78         5.98         6.41         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  DDX43 MUTATED DDX43 WILD-TYPE 
           0.99            0.13 
  DDX43 MUTATED DDX43 WILD-TYPE 
          60.49          125.65 
  DDX43 MUTATED DDX43 WILD-TYPE 
          10.34           17.64 
[1] "1.0 - 60.5 (10.3)"  "0.1 - 125.7 (17.6)"
[1] "hr=" "1.8"
D134V2, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     5   6
  DDX43 WILD-TYPE 124 135
  DDX43 MUTATED DDX43 WILD-TYPE 
             11             259 
  DDX43 MUTATED DDX43 WILD-TYPE 
              6             135 
$`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       134.40 
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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        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       195.02        17.92       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  DDX43 MUTATED DDX43 WILD-TYPE 
          12.59            0.16 
  DDX43 MUTATED DDX43 WILD-TYPE 
         134.40          357.37 
  DDX43 MUTATED DDX43 WILD-TYPE 
          46.82           53.19 
[1] "12.6 - 134.4 (46.8)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1.6"
D134V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DDX43 MUTATED                    0             0
  DDX43 WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DDX43 MUTATED                                           2                   9
  DDX43 WILD-TYPE                                        58                 162
D134V4, multiclass
                                           clus
vv                                          DDX43 MUTATED DDX43 WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   9             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
  DDX43 MUTATED             0       0       1        0        1        2
  DDX43 WILD-TYPE          10       6      23       10       23       14
                 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        30         13         22
                 vv
clus              STAGE IIIC STAGE IV
  DDX43 MUTATED            2        0
  DDX43 WILD-TYPE         44       16
D134V5, multiclass
             clus
vv            DDX43 MUTATED DDX43 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              14
  STAGE IIA               1               9
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              0              13
  STAGE IIIB              1              22
  STAGE IIIC              2              44
  STAGE IV                0              16
[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    52 55 50 57
D134V6, multiclass
       clus
vv      DDX43 MUTATED DDX43 WILD-TYPE
  T0+T1             0              52
  T2                4              55
  T3                4              50
  T4                0              57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDX43 MUTATED     5   3   2   1
  DDX43 WILD-TYPE 134  45  31  35
D134V7, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0             5             134
  N1             3              45
  N2             2              31
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DDX43 MUTATED    11   0   0   0   0
  DDX43 WILD-TYPE 233   4   3   2   8
D134V8, multiclass
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  M0             11             233
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 99 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      4    3
  DDX43 WILD-TYPE   99   65
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO              4              99
  YES             3              65
[1] 2 2
[1] FALSE
D134V10, binary
                 cls
clus                0   1
  DDX43 MUTATED     1  10
  DDX43 WILD-TYPE  35 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      1   10
  DDX43 WILD-TYPE   35  229
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO              1              35
  YES            10             229
[1] 2 2
[1] FALSE
D134V11, continuous
D134V12, binary
                 cls
clus                0   1
  DDX43 MUTATED     4   7
  DDX43 WILD-TYPE 102 163
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      4    7
  DDX43 WILD-TYPE  102  163
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  FEMALE             4             102
  MALE               7             163
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX43 MUTATED       0                         0    11
  DDX43 WILD-TYPE     3                         1   261
D134V13, multiclass
                           clus
vv                          DDX43 MUTATED DDX43 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             261
[1] 3 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   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      0   11
  DDX43 WILD-TYPE    3  258
                        clus
vv                       DDX43 MUTATED DDX43 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             258
[1] 2 2
[1] FALSE

Clustering(135) Variable = CYP3A7 MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2                0   1
  CYP3A7 MUTATED    11  13
  CYP3A7 WILD-TYPE 115 127
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              24              242 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              13              127 
$`CYP3A7 MUTATED`
TCGA-D3-A2JF TCGA-D3-A3MR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-EE-A180 
       44.19       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        62.79         2.43         8.09        60.00        55.69 
TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A3AA TCGA-EE-A3AC TCGA-ER-A2NH TCGA-FS-A1ZF 
        2.73        63.42       124.31        51.62        11.74        11.08 
TCGA-FS-A1ZK TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A266 
       12.89         5.23        14.20         0.99        11.61        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        86.76        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 
       59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       17.72        23.11        21.93         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        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        13.22        11.57        10.55         6.31 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        36.85         1.08        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A2A0 
       12.03         8.09         8.84         9.99        32.15        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        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-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       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       53.16        52.67         5.56       122.73         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.39         0.82        53.85         7.36        28.73        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 
       17.33         9.90         7.23         0.85        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
            0.99             0.13 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          124.31           125.65 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          12.315           17.640 
[1] "1.0 - 124.3 (12.3)" "0.1 - 125.7 (17.6)"
[1] "hr=" "1"  
D135V2, survival
                  sevent
clus2                0   1
  CYP3A7 MUTATED    11  13
  CYP3A7 WILD-TYPE 118 128
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              24              246 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              13              128 
$`CYP3A7 MUTATED`
TCGA-D3-A2JF TCGA-D3-A3MR TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-EE-A180 
       62.07       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        63.78        25.87        17.92       161.03       126.81 
TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A3AA TCGA-EE-A3AC TCGA-ER-A2NH TCGA-FS-A1ZF 
      268.73        96.23       124.31        51.62        32.05        15.45 
TCGA-FS-A1ZK TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GF-A6C9 TCGA-GN-A266 
       23.93        27.02       174.84        22.92        11.74        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        86.76        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 
       59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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 
       22.29         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        68.25        54.02        17.29 
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       133.81       151.27        91.56       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 
       64.64         2.60        56.84        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       195.02        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
       39.29        86.14        59.28        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       158.63       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       134.40       162.48        71.21 
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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        16.37        31.27       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
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-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-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67        28.73        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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23         2.04       139.89       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
           10.13             0.16 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          268.73           357.37 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          42.460           53.175 
[1] "10.1 - 268.7 (42.5)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1.1"
D135V3, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  CYP3A7 MUTATED                    8             0
  CYP3A7 WILD-TYPE                 31             5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  CYP3A7 MUTATED                                           3
  CYP3A7 WILD-TYPE                                        57
                  vv
clus               REGIONAL LYMPH NODE
  CYP3A7 MUTATED                    14
  CYP3A7 WILD-TYPE                 157
D135V4, multiclass
                                           clus
vv                                          CYP3A7 MUTATED CYP3A7 WILD-TYPE
  DISTANT METASTASIS                                     8               31
  PRIMARY TUMOR                                          0                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              3               57
  REGIONAL LYMPH NODE                                   14              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       3        1        1        3
  CYP3A7 WILD-TYPE           9       6      21        9       23       13
                  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        26         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CYP3A7 MUTATED            4          3        0
  CYP3A7 WILD-TYPE         19         43       16
D135V5, multiclass
             clus
vv            CYP3A7 MUTATED CYP3A7 WILD-TYPE
  I OR II NOS              1                9
  STAGE 0                  0                6
  STAGE I                  3               21
  STAGE IA                 1                9
  STAGE IB                 1               23
  STAGE II                 3               13
  STAGE IIA                0               10
  STAGE IIB                1               13
  STAGE IIC                1                8
  STAGE III                6               26
  STAGE IIIA               0               13
  STAGE IIIB               4               19
  STAGE IIIC               3               43
  STAGE IV                 0               16
[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  5  5  5
  CYP3A7 WILD-TYPE    45 54 49 52
D135V6, multiclass
       clus
vv      CYP3A7 MUTATED CYP3A7 WILD-TYPE
  T0+T1              7               45
  T2                 5               54
  T3                 5               49
  T4                 5               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
  CYP3A7 MUTATED    13   4   4   2
  CYP3A7 WILD-TYPE 126  44  29  34
D135V7, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  N0             13              126
  N1              4               44
  N2              4               29
  N3              2               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                M0  M1 M1A M1B M1C
  CYP3A7 MUTATED    23   0   0   0   0
  CYP3A7 WILD-TYPE 221   4   3   2   8
D135V8, multiclass
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  M0              23              221
  M1               0                4
  M1A              0                3
  M1B              0                2
  M1C              0                8
[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 94 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      9    3
  CYP3A7 WILD-TYPE   94   65
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  NO               9               94
  YES              3               65
[1] 2 2
[1] FALSE
D135V10, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     6  19
  CYP3A7 WILD-TYPE  30 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      6   19
  CYP3A7 WILD-TYPE   30  220
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  NO               6               30
  YES             19              220
[1] 2 2
[1] FALSE
D135V11, continuous
D135V12, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     9  16
  CYP3A7 WILD-TYPE  97 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      9   16
  CYP3A7 WILD-TYPE   97  154
        clus
vv       CYP3A7 MUTATED CYP3A7 WILD-TYPE
  FEMALE              9               97
  MALE               16              154
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP3A7 MUTATED       0                         0    25
  CYP3A7 WILD-TYPE     3                         1   247
D135V13, multiclass
                           clus
vv                          CYP3A7 MUTATED CYP3A7 WILD-TYPE
  ASIAN                                  0                3
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 25              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"
D135V14, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     1  24
  CYP3A7 WILD-TYPE   2 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      1   24
  CYP3A7 WILD-TYPE    2  245
                        clus
vv                       CYP3A7 MUTATED CYP3A7 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             24              245
[1] 2 2
[1] FALSE

Clustering(136) Variable = VGLL1 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2               0   1
  VGLL1 MUTATED     4   2
  VGLL1 WILD-TYPE 122 138
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             260 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              2             138 
$`VGLL1 MUTATED`
TCGA-EE-A2GP TCGA-EE-A2MS TCGA-ER-A1A1 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GN-A266 
        5.42        53.16        78.44         0.99        17.33        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87        13.68        17.72        23.11         4.01        21.93 
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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        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        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       60.49        52.67         5.56       124.31       122.73        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        6.58        17.72        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        5.62        18.41        85.74        15.72        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-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  VGLL1 MUTATED VGLL1 WILD-TYPE 
           0.99            0.13 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
          78.44          125.65 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
         13.730          17.015 
[1] "1.0 - 78.4 (13.7)"  "0.1 - 125.7 (17.0)"
[1] "hr=" "1.5"
D136V2, survival
                 sevent
clus2               0   1
  VGLL1 MUTATED     4   2
  VGLL1 WILD-TYPE 125 139
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              6             264 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              2             139 
$`VGLL1 MUTATED`
TCGA-EE-A2GP TCGA-EE-A2MS TCGA-ER-A1A1 TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GN-A266 
       13.91       162.48        79.99        22.92        19.30        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56 
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 
       63.78        72.07        64.64         2.60        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       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       126.81 
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-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
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       158.63       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       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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-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-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2.04        11.74       139.89       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  VGLL1 MUTATED VGLL1 WILD-TYPE 
          10.13            0.16 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
         162.48          357.37 
  VGLL1 MUTATED VGLL1 WILD-TYPE 
         21.110          52.585 
[1] "10.1 - 162.5 (21.1)" "0.2 - 357.4 (52.6)" 
[1] "hr=" "1.1"
D136V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  VGLL1 MUTATED                    0             0
  VGLL1 WILD-TYPE                 39             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  VGLL1 MUTATED                                           2                   4
  VGLL1 WILD-TYPE                                        58                 167
D136V4, multiclass
                                           clus
vv                                          VGLL1 MUTATED VGLL1 WILD-TYPE
  DISTANT METASTASIS                                    0              39
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   4             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
  VGLL1 MUTATED             0       0       0        0        0        1
  VGLL1 WILD-TYPE          10       6      24       10       24       15
                 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        30         13         22
                 vv
clus              STAGE IIIC STAGE IV
  VGLL1 MUTATED            1        0
  VGLL1 WILD-TYPE         45       16
D136V5, multiclass
             clus
vv            VGLL1 MUTATED VGLL1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 0              24
  STAGE IA                0              10
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               2              30
  STAGE IIIA              0              13
  STAGE IIIB              1              22
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    52 59 52 56
D136V6, multiclass
       clus
vv      VGLL1 MUTATED VGLL1 WILD-TYPE
  T0+T1             0              52
  T2                0              59
  T3                2              52
  T4                1              56
[1] 4 2
[1] TRUE
[1] "dimension of 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 138  46  32  35
D136V7, multiclass
    clus
vv   VGLL1 MUTATED VGLL1 WILD-TYPE
  N0             1             138
  N1             2              46
  N2             1              32
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  VGLL1 MUTATED     4   0   0   0   0
  VGLL1 WILD-TYPE 240   4   3   2   8
D136V8, multiclass
     clus
vv    VGLL1 MUTATED VGLL1 WILD-TYPE
  M0              4             240
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 102  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      1    1
  VGLL1 WILD-TYPE  102   67
     clus
vv    VGLL1 MUTATED VGLL1 WILD-TYPE
  NO              1             102
  YES             1              67
[1] 2 2
[1] FALSE
D136V10, binary
                 cls
clus                0   1
  VGLL1 MUTATED     2   4
  VGLL1 WILD-TYPE  34 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      2    4
  VGLL1 WILD-TYPE   34  235
     clus
vv    VGLL1 MUTATED VGLL1 WILD-TYPE
  NO              2              34
  YES             4             235
[1] 2 2
[1] FALSE
D136V11, continuous
[1] "Remove cluster labels:" "VGLL1 MUTATED"         
clus
  VGLL1 MUTATED VGLL1 WILD-TYPE 
              2             202 
     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-A2MF      TCGA-EE-A2MG      TCGA-EE-A2MH      TCGA-EE-A2MI 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2MJ      TCGA-EE-A2MK      TCGA-EE-A2ML      TCGA-EE-A2MM 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2MN      TCGA-EE-A2MP      TCGA-EE-A2MQ      TCGA-EE-A2MR 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A2MT      TCGA-EE-A2MU      TCGA-EE-A3AE      TCGA-EE-A3AH 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A3J3      TCGA-EE-A3J4      TCGA-EE-A3J5      TCGA-EE-A3J7 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A3J8      TCGA-EE-A3JA      TCGA-EE-A3JB      TCGA-EE-A3JE 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-EE-A3JH      TCGA-EE-A3JI      TCGA-ER-A197      TCGA-ER-A198 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A199      TCGA-ER-A19C      TCGA-ER-A19D      TCGA-ER-A19E 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A19F      TCGA-ER-A19G      TCGA-ER-A19H      TCGA-ER-A19M 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A19Q      TCGA-ER-A19T      TCGA-ER-A19W      TCGA-ER-A2NC 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A2ND      TCGA-ER-A2NF      TCGA-ER-A2NG      TCGA-ER-A2NH 
"VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" "VGLL1 WILD-TYPE" 
     TCGA-ER-A3ET      TCGA-ER-A3EV      TCGA-ER-A3PL      TCGA-ER-A42K 
"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 105 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      1    5
  VGLL1 WILD-TYPE  105  165
        clus
vv       VGLL1 MUTATED VGLL1 WILD-TYPE
  FEMALE             1             105
  MALE               5             165
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VGLL1 MUTATED       0                         0     6
  VGLL1 WILD-TYPE     3                         1   266
D136V13, multiclass
                           clus
vv                          VGLL1 MUTATED VGLL1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 6             266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V14, binary
                 cls
clus                0   1
  VGLL1 MUTATED     0   6
  VGLL1 WILD-TYPE   3 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VGLL1 MUTATED      0    6
  VGLL1 WILD-TYPE    3  263
                        clus
vv                       VGLL1 MUTATED VGLL1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             263
[1] 2 2
[1] FALSE

Clustering(137) Variable = GML MUTATION ANALYSIS
D137V1, survival
               sevent
clus2             0   1
  GML MUTATED     4   5
  GML WILD-TYPE 122 135
  GML MUTATED GML WILD-TYPE 
            9           257 
  GML MUTATED GML WILD-TYPE 
            5           135 
$`GML MUTATED`
TCGA-D3-A2JC TCGA-DA-A1I7 TCGA-EB-A5UL TCGA-EE-A29D TCGA-EE-A2GJ TCGA-EE-A2MI 
       86.76        36.69        13.35        11.15        19.43        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-FS-A1Z3 
       63.42        52.67        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        44.19 
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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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        23.15        19.00        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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 
       60.49        53.16         5.56       124.31       122.73        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-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-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       12.16        14.70         5.79         0.33         0.69 

  GML MUTATED GML WILD-TYPE 
        11.15          0.13 
  GML MUTATED GML WILD-TYPE 
        86.76        125.65 
  GML MUTATED GML WILD-TYPE 
        19.43         16.47 
[1] "11.2 - 86.8 (19.4)" "0.1 - 125.7 (16.5)"
[1] "hr=" "1.2"
D137V2, survival
               sevent
clus2             0   1
  GML MUTATED     5   5
  GML WILD-TYPE 124 136
  GML MUTATED GML WILD-TYPE 
           10           260 
  GML MUTATED GML WILD-TYPE 
            5           136 
$`GML MUTATED`
TCGA-D3-A2JC TCGA-D9-A1JW TCGA-DA-A1I7 TCGA-EB-A5UL TCGA-EE-A29D TCGA-EE-A2GJ 
       86.76         3.65        61.18        17.29        13.97        89.33 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-FS-A1Z3 
      204.66        96.23        71.21        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        62.07 
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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX 
      178.32        18.18       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        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       54.02        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        63.78        72.07        64.64         2.60        56.84 
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 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       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       126.81 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73       103.20        16.96       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       47.54       248.65        43.23       134.40       162.48        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.72       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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  GML MUTATED GML WILD-TYPE 
         3.65          0.16 
  GML MUTATED GML WILD-TYPE 
       204.66        357.37 
  GML MUTATED GML WILD-TYPE 
       66.195        51.485 
[1] "3.6 - 204.7 (66.2)" "0.2 - 357.4 (51.5)"
[1] "hr=" "1"  
D137V3, continuous
               vv
clus            DISTANT METASTASIS PRIMARY TUMOR
  GML MUTATED                    1             0
  GML WILD-TYPE                 38             5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  GML MUTATED                                           1                   8
  GML WILD-TYPE                                        59                 163
D137V4, multiclass
                                           clus
vv                                          GML MUTATED GML WILD-TYPE
  DISTANT METASTASIS                                  1            38
  PRIMARY TUMOR                                       0             5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           1            59
  REGIONAL LYMPH NODE                                 8           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
  GML MUTATED             0       0       0        1        1        0
  GML WILD-TYPE          10       6      24        9       23       16
               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        29         13         22
               vv
clus            STAGE IIIC STAGE IV
  GML MUTATED            1        1
  GML WILD-TYPE         45       15
D137V5, multiclass
             clus
vv            GML MUTATED GML WILD-TYPE
  I OR II NOS           0            10
  STAGE 0               0             6
  STAGE I               0            24
  STAGE IA              1             9
  STAGE IB              1            23
  STAGE II              0            16
  STAGE IIA             0            10
  STAGE IIB             1            13
  STAGE IIC             0             9
  STAGE III             3            29
  STAGE IIIA            0            13
  STAGE IIIB            1            22
  STAGE IIIC            1            45
  STAGE IV              1            15
[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    48 58 53 55
D137V6, multiclass
       clus
vv      GML MUTATED GML WILD-TYPE
  T0+T1           4            48
  T2              1            58
  T3              1            53
  T4              2            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
  GML MUTATED     5   2   3   0
  GML WILD-TYPE 134  46  30  36
D137V7, multiclass
    clus
vv   GML MUTATED GML WILD-TYPE
  N0           5           134
  N1           2            46
  N2           3            30
  N3           0            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             M0  M1 M1A M1B M1C
  GML MUTATED     9   1   0   0   0
  GML WILD-TYPE 235   3   3   2   8
D137V8, multiclass
     clus
vv    GML MUTATED GML WILD-TYPE
  M0            9           235
  M1            1             3
  M1A           0             3
  M1B           0             2
  M1C           0             8
[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 99 67
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      4    1
  GML WILD-TYPE   99   67
     clus
vv    GML MUTATED GML WILD-TYPE
  NO            4            99
  YES           1            67
[1] 2 2
[1] FALSE
D137V10, binary
               cls
clus              0   1
  GML MUTATED     3   7
  GML WILD-TYPE  33 232
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      3    7
  GML WILD-TYPE   33  232
     clus
vv    GML MUTATED GML WILD-TYPE
  NO            3            33
  YES           7           232
[1] 2 2
[1] FALSE
D137V11, continuous
D137V12, binary
               cls
clus              0   1
  GML MUTATED     2   8
  GML WILD-TYPE 104 162
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      2    8
  GML WILD-TYPE  104  162
        clus
vv       GML MUTATED GML WILD-TYPE
  FEMALE           2           104
  MALE             8           162
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GML MUTATED       0                         0    10
  GML WILD-TYPE     3                         1   262
D137V13, multiclass
                           clus
vv                          GML MUTATED GML WILD-TYPE
  ASIAN                               0             3
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              10           262
[1] 3 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   3 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      0   10
  GML WILD-TYPE    3  259
                        clus
vv                       GML MUTATED GML WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          10           259
[1] 2 2
[1] FALSE

Clustering(138) Variable = GZMA MUTATION ANALYSIS
D138V1, survival
                sevent
clus2              0   1
  GZMA MUTATED     7   4
  GZMA WILD-TYPE 119 136
  GZMA MUTATED GZMA WILD-TYPE 
            11            255 
  GZMA MUTATED GZMA WILD-TYPE 
             4            136 
$`GZMA MUTATED`
TCGA-D3-A3CB TCGA-DA-A1I8 TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2A2 TCGA-EE-A2GC 
       82.29        25.15        62.79        36.85        36.30        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         1.08        39.62         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        32.15         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        36.33        51.12        17.98        60.00 
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-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
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        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
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-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
        5.79         0.33         0.69 

  GZMA MUTATED GZMA WILD-TYPE 
          0.99           0.13 
  GZMA MUTATED GZMA WILD-TYPE 
         82.29         125.65 
  GZMA MUTATED GZMA WILD-TYPE 
         30.08          16.14 
[1] "1.0 - 82.3 (30.1)"  "0.1 - 125.7 (16.1)"
[1] "hr=" "1.7"
D138V2, survival
                sevent
clus2              0   1
  GZMA MUTATED     7   4
  GZMA WILD-TYPE 122 137
  GZMA MUTATED GZMA WILD-TYPE 
            11            259 
  GZMA MUTATED GZMA WILD-TYPE 
             4            137 
$`GZMA MUTATED`
TCGA-D3-A3CB TCGA-DA-A1I8 TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2A2 TCGA-EE-A2GC 
      166.52        53.92        63.78        64.64        36.82        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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 
       56.84        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       195.02        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 
       86.14        59.28       314.56       161.03       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       126.81        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-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       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       158.63       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       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-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        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  GZMA MUTATED GZMA WILD-TYPE 
         10.13           0.16 
  GZMA MUTATED GZMA WILD-TYPE 
        166.52         357.37 
  GZMA MUTATED GZMA WILD-TYPE 
         48.72          52.01 
[1] "10.1 - 166.5 (48.7)" "0.2 - 357.4 (52.0)" 
[1] "hr=" "1.1"
D138V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  GZMA MUTATED                    0             0
  GZMA WILD-TYPE                 39             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  GZMA MUTATED                                           4                   7
  GZMA WILD-TYPE                                        56                 164
D138V4, multiclass
                                           clus
vv                                          GZMA MUTATED GZMA WILD-TYPE
  DISTANT METASTASIS                                   0             39
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            4             56
  REGIONAL LYMPH NODE                                  7            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
  GZMA MUTATED             1       0       0        2        1        1
  GZMA WILD-TYPE           9       6      24        8       23       15
                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        31         13         22
                vv
clus             STAGE IIIC STAGE IV
  GZMA MUTATED            2        0
  GZMA WILD-TYPE         44       16
D138V5, multiclass
             clus
vv            GZMA MUTATED GZMA WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                0             24
  STAGE IA               2              8
  STAGE IB               1             23
  STAGE II               1             15
  STAGE IIA              0             10
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              1             31
  STAGE IIIA             0             13
  STAGE IIIB             1             22
  STAGE IIIC             2             44
  STAGE IV               0             16
[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    50 57 52 54
D138V6, multiclass
       clus
vv      GZMA MUTATED GZMA WILD-TYPE
  T0+T1            2             50
  T2               2             57
  T3               2             52
  T4               3             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
  GZMA MUTATED     6   2   1   1
  GZMA WILD-TYPE 133  46  32  35
D138V7, multiclass
    clus
vv   GZMA MUTATED GZMA WILD-TYPE
  N0            6            133
  N1            2             46
  N2            1             32
  N3            1             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              M0  M1 M1A M1B M1C
  GZMA MUTATED    10   0   0   0   0
  GZMA WILD-TYPE 234   4   3   2   8
D138V8, multiclass
     clus
vv    GZMA MUTATED GZMA WILD-TYPE
  M0            10            234
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 99 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      4    3
  GZMA WILD-TYPE   99   65
     clus
vv    GZMA MUTATED GZMA WILD-TYPE
  NO             4             99
  YES            3             65
[1] 2 2
[1] FALSE
D138V10, binary
                cls
clus               0   1
  GZMA MUTATED     1  10
  GZMA WILD-TYPE  35 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      1   10
  GZMA WILD-TYPE   35  229
     clus
vv    GZMA MUTATED GZMA WILD-TYPE
  NO             1             35
  YES           10            229
[1] 2 2
[1] FALSE
D138V11, continuous
D138V12, binary
                cls
clus               0   1
  GZMA MUTATED     3   8
  GZMA WILD-TYPE 103 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      3    8
  GZMA WILD-TYPE  103  162
        clus
vv       GZMA MUTATED GZMA WILD-TYPE
  FEMALE            3            103
  MALE              8            162
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GZMA MUTATED       0                         0    11
  GZMA WILD-TYPE     3                         1   261
D138V13, multiclass
                           clus
vv                          GZMA MUTATED GZMA WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               11            261
[1] 3 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   3 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZMA MUTATED      0   11
  GZMA WILD-TYPE    3  258
                        clus
vv                       GZMA MUTATED GZMA WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           11            258
[1] 2 2
[1] FALSE

Clustering(139) Variable = NPTX1 MUTATION ANALYSIS
D139V1, survival
                 sevent
clus2               0   1
  NPTX1 MUTATED     6   2
  NPTX1 WILD-TYPE 120 138
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             258 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              2             138 
$`NPTX1 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2MR 
       44.19        13.22        11.15         1.08        30.08        60.49 
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        86.76        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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55        36.85        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        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       125.65       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        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  NPTX1 MUTATED NPTX1 WILD-TYPE 
           0.99            0.13 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          60.49          125.65 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
          21.65           16.90 
[1] "1.0 - 60.5 (21.6)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "2"  
D139V2, survival
                 sevent
clus2               0   1
  NPTX1 MUTATED     6   2
  NPTX1 WILD-TYPE 123 139
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              8             262 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
              2             139 
$`NPTX1 MUTATED`
TCGA-D3-A2JF TCGA-D9-A6EC TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A2GI TCGA-EE-A2MR 
       62.07        66.25        13.97         2.60        48.72       134.40 
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        86.76        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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       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 
      158.63       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 
      162.48        71.21        53.26       124.31       122.73        51.62 
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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
       39.58         6.67         0.33         0.69 

  NPTX1 MUTATED NPTX1 WILD-TYPE 
           2.60            0.16 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
         134.40          357.37 
  NPTX1 MUTATED NPTX1 WILD-TYPE 
         51.615          51.815 
[1] "2.6 - 134.4 (51.6)" "0.2 - 357.4 (51.8)"
[1] "hr=" "1.5"
D139V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  NPTX1 MUTATED                    1             1
  NPTX1 WILD-TYPE                 38             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  NPTX1 MUTATED                                           0                   6
  NPTX1 WILD-TYPE                                        60                 165
D139V4, multiclass
                                           clus
vv                                          NPTX1 MUTATED NPTX1 WILD-TYPE
  DISTANT METASTASIS                                    1              38
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             0              60
  REGIONAL LYMPH NODE                                   6             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
  NPTX1 MUTATED             0       0       1        3        0        0
  NPTX1 WILD-TYPE          10       6      23        7       24       16
                 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        31         12         23
                 vv
clus              STAGE IIIC STAGE IV
  NPTX1 MUTATED            2        0
  NPTX1 WILD-TYPE         44       16
D139V5, multiclass
             clus
vv            NPTX1 MUTATED NPTX1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                3               7
  STAGE IB                0              24
  STAGE II                0              16
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               0               9
  STAGE III               1              31
  STAGE IIIA              1              12
  STAGE IIIB              0              23
  STAGE IIIC              2              44
  STAGE IV                0              16
[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    49 58 52 56
D139V6, multiclass
       clus
vv      NPTX1 MUTATED NPTX1 WILD-TYPE
  T0+T1             3              49
  T2                1              58
  T3                2              52
  T4                1              56
[1] 4 2
[1] TRUE
[1] "dimension of 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 135  46  32  35
D139V7, multiclass
    clus
vv   NPTX1 MUTATED NPTX1 WILD-TYPE
  N0             4             135
  N1             2              46
  N2             1              32
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  NPTX1 MUTATED     8   0   0   0   0
  NPTX1 WILD-TYPE 236   4   3   2   8
D139V8, multiclass
     clus
vv    NPTX1 MUTATED NPTX1 WILD-TYPE
  M0              8             236
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 98 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      5    2
  NPTX1 WILD-TYPE   98   66
     clus
vv    NPTX1 MUTATED NPTX1 WILD-TYPE
  NO              5              98
  YES             2              66
[1] 2 2
[1] FALSE
D139V10, binary
                 cls
clus                0   1
  NPTX1 MUTATED     0   8
  NPTX1 WILD-TYPE  36 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      0    8
  NPTX1 WILD-TYPE   36  231
     clus
vv    NPTX1 MUTATED NPTX1 WILD-TYPE
  NO              0              36
  YES             8             231
[1] 2 2
[1] FALSE
D139V11, continuous
D139V12, binary
                 cls
clus                0   1
  NPTX1 MUTATED     2   6
  NPTX1 WILD-TYPE 104 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      2    6
  NPTX1 WILD-TYPE  104  164
        clus
vv       NPTX1 MUTATED NPTX1 WILD-TYPE
  FEMALE             2             104
  MALE               6             164
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPTX1 MUTATED       0                         0     8
  NPTX1 WILD-TYPE     3                         1   264
D139V13, multiclass
                           clus
vv                          NPTX1 MUTATED NPTX1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             264
[1] 3 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   3 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPTX1 MUTATED      0    8
  NPTX1 WILD-TYPE    3  261
                        clus
vv                       NPTX1 MUTATED NPTX1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             261
[1] 2 2
[1] FALSE

Clustering(140) Variable = DACT1 MUTATION ANALYSIS
D140V1, survival
                 sevent
clus2               0   1
  DACT1 MUTATED     5   7
  DACT1 WILD-TYPE 121 133
  DACT1 MUTATED DACT1 WILD-TYPE 
             12             254 
  DACT1 MUTATED DACT1 WILD-TYPE 
              7             133 
$`DACT1 MUTATED`
TCGA-D3-A3MR TCGA-EE-A2GN TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AF 
      103.59        33.83         2.73        14.56        63.42        13.81 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-FS-A1YY TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A6C9 
       27.35        21.73        11.01         0.99        17.33        11.61 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL 
       14.83        13.15         0.20        23.15        19.00        13.35 
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        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         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        62.79         8.55        36.85         1.08        39.62 
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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        28.31        55.69 
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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       44.25         7.96       125.65       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        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
      124.31       122.73        51.62         3.68        30.15        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.95        18.41        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        64.47 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        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-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  DACT1 MUTATED DACT1 WILD-TYPE 
           0.99            0.13 
  DACT1 MUTATED DACT1 WILD-TYPE 
         103.59          125.65 
  DACT1 MUTATED DACT1 WILD-TYPE 
         15.945          17.015 
[1] "1.0 - 103.6 (15.9)" "0.1 - 125.7 (17.0)"
[1] "hr=" "1.1"
D140V2, survival
                 sevent
clus2               0   1
  DACT1 MUTATED     5   7
  DACT1 WILD-TYPE 124 134
  DACT1 MUTATED DACT1 WILD-TYPE 
             12             258 
  DACT1 MUTATED DACT1 WILD-TYPE 
              7             134 
$`DACT1 MUTATED`
TCGA-D3-A3MR TCGA-EE-A2GN TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AF 
      103.59        90.97       268.73       204.66        96.23        13.81 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-FS-A1YY TCGA-FW-A3R5 TCGA-FW-A5DY TCGA-GF-A6C9 
       27.35       109.58       228.59        22.92        19.30        11.74 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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        68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       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       126.81        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 
      158.63       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 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       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-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       92.98       174.21        15.72       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-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-A266 TCGA-GN-A267 
        2.04       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       62.79        32.48        39.58         6.67         0.33         0.69 

  DACT1 MUTATED DACT1 WILD-TYPE 
          11.74            0.16 
  DACT1 MUTATED DACT1 WILD-TYPE 
         268.73          357.37 
  DACT1 MUTATED DACT1 WILD-TYPE 
         93.600          51.485 
[1] "11.7 - 268.7 (93.6)" "0.2 - 357.4 (51.5)" 
[1] "hr=" "1.3"
D140V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  DACT1 MUTATED                    2             0
  DACT1 WILD-TYPE                 37             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  DACT1 MUTATED                                           3                   8
  DACT1 WILD-TYPE                                        57                 163
D140V4, multiclass
                                           clus
vv                                          DACT1 MUTATED DACT1 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             3              57
  REGIONAL LYMPH NODE                                   8             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       1        0        1        0
  DACT1 WILD-TYPE          10       5      23       10       23       16
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DACT1 MUTATED           2         1         0         5          0          1
  DACT1 WILD-TYPE         8        13         9        27         13         22
                 vv
clus              STAGE IIIC STAGE IV
  DACT1 MUTATED            1        0
  DACT1 WILD-TYPE         45       16
D140V5, multiclass
             clus
vv            DACT1 MUTATED DACT1 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 1              23
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                0              16
  STAGE IIA               2               8
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               5              27
  STAGE IIIA              0              13
  STAGE IIIB              1              22
  STAGE IIIC              1              45
  STAGE IV                0              16
[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  3  2  2
  DACT1 WILD-TYPE    50 56 52 55
D140V6, multiclass
       clus
vv      DACT1 MUTATED DACT1 WILD-TYPE
  T0+T1             2              50
  T2                3              56
  T3                2              52
  T4                2              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
  DACT1 MUTATED     7   2   2   1
  DACT1 WILD-TYPE 132  46  31  35
D140V7, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  N0             7             132
  N1             2              46
  N2             2              31
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  DACT1 MUTATED    11   0   0   0   0
  DACT1 WILD-TYPE 233   4   3   2   8
D140V8, multiclass
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  M0             11             233
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 101  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      2    1
  DACT1 WILD-TYPE  101   67
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  NO              2             101
  YES             1              67
[1] 2 2
[1] FALSE
D140V10, binary
                 cls
clus                0   1
  DACT1 MUTATED     4   9
  DACT1 WILD-TYPE  32 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      4    9
  DACT1 WILD-TYPE   32  230
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  NO              4              32
  YES             9             230
[1] 2 2
[1] FALSE
D140V11, continuous
D140V12, binary
                 cls
clus                0   1
  DACT1 MUTATED     4   9
  DACT1 WILD-TYPE 102 161
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      4    9
  DACT1 WILD-TYPE  102  161
        clus
vv       DACT1 MUTATED DACT1 WILD-TYPE
  FEMALE             4             102
  MALE               9             161
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DACT1 MUTATED       0                         0    13
  DACT1 WILD-TYPE     3                         1   259
D140V13, multiclass
                           clus
vv                          DACT1 MUTATED DACT1 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             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"
D140V14, binary
                 cls
clus                0   1
  DACT1 MUTATED     0  13
  DACT1 WILD-TYPE   3 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      0   13
  DACT1 WILD-TYPE    3  256
                        clus
vv                       DACT1 MUTATED DACT1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             256
[1] 2 2
[1] FALSE

Clustering(141) Variable = STK19 MUTATION ANALYSIS
D141V1, survival
                 sevent
clus2               0   1
  STK19 MUTATED     5   8
  STK19 WILD-TYPE 121 132
  STK19 MUTATED STK19 WILD-TYPE 
             13             253 
  STK19 MUTATED STK19 WILD-TYPE 
              8             132 
$`STK19 MUTATED`
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       21.93        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-GF-A6C9 
       17.98        30.08        44.25        33.60         7.30        11.61 
TCGA-GN-A266 
       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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 
       47.87        13.68        17.72        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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B 
       10.55         6.31         8.12         1.35         5.13        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         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        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         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        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        36.33        51.12        34.29        60.00        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        55.69 
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-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73         7.96        14.56        63.42       125.65       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        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        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-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        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-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41        85.74        15.72        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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       16.24        15.42        12.16        14.70         5.79         0.33 
TCGA-RP-A694 
        0.69 

  STK19 MUTATED STK19 WILD-TYPE 
           1.12            0.13 
  STK19 MUTATED STK19 WILD-TYPE 
          48.79          125.65 
  STK19 MUTATED STK19 WILD-TYPE 
          13.22           17.33 
[1] "1.1 - 48.8 (13.2)"  "0.1 - 125.7 (17.3)"
[1] "hr=" "1.4"
D141V2, survival
                 sevent
clus2               0   1
  STK19 MUTATED     5   8
  STK19 WILD-TYPE 124 133
  STK19 MUTATED STK19 WILD-TYPE 
             13             257 
  STK19 MUTATED STK19 WILD-TYPE 
              8             133 
$`STK19 MUTATED`
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       22.29        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-GF-A6C9 
      314.56        48.72       103.20       148.08        27.72        11.74 
TCGA-GN-A266 
       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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       178.32        18.18       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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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       133.81       151.27        91.56 
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 
       63.78        72.07        64.64         2.60        56.84        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       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28        67.43       161.03       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       126.81        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-A2MF TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       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       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       80.32        46.98        33.21         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.72       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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       32.48        39.58         6.67         0.33         0.69 

  STK19 MUTATED STK19 WILD-TYPE 
           4.96            0.16 
  STK19 MUTATED STK19 WILD-TYPE 
         314.56          357.37 
  STK19 MUTATED STK19 WILD-TYPE 
          33.73           53.19 
[1] "5.0 - 314.6 (33.7)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.2"
D141V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  STK19 MUTATED                    2             1
  STK19 WILD-TYPE                 37             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  STK19 MUTATED                                           2                   8
  STK19 WILD-TYPE                                        58                 163
D141V4, multiclass
                                           clus
vv                                          STK19 MUTATED STK19 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             2              58
  REGIONAL LYMPH NODE                                   8             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
  STK19 MUTATED             0       1       2        1        0        1
  STK19 WILD-TYPE          10       5      22        9       24       15
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  STK19 MUTATED           0         1         0         0          1          4
  STK19 WILD-TYPE        10        13         9        32         12         19
                 vv
clus              STAGE IIIC STAGE IV
  STK19 MUTATED            1        0
  STK19 WILD-TYPE         45       16
D141V5, multiclass
             clus
vv            STK19 MUTATED STK19 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 2              22
  STAGE IA                1               9
  STAGE IB                0              24
  STAGE II                1              15
  STAGE IIA               0              10
  STAGE IIB               1              13
  STAGE IIC               0               9
  STAGE III               0              32
  STAGE IIIA              1              12
  STAGE IIIB              4              19
  STAGE IIIC              1              45
  STAGE IV                0              16
[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    50 57 51 54
D141V6, multiclass
       clus
vv      STK19 MUTATED STK19 WILD-TYPE
  T0+T1             2              50
  T2                2              57
  T3                3              51
  T4                3              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
  STK19 MUTATED     6   2   2   1
  STK19 WILD-TYPE 133  46  31  35
D141V7, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  N0             6             133
  N1             2              46
  N2             2              31
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  STK19 MUTATED    11   0   0   0   0
  STK19 WILD-TYPE 233   4   3   2   8
D141V8, multiclass
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  M0             11             233
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 99 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      4    3
  STK19 WILD-TYPE   99   65
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              4              99
  YES             3              65
[1] 2 2
[1] FALSE
D141V10, binary
                 cls
clus                0   1
  STK19 MUTATED     3  10
  STK19 WILD-TYPE  33 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      3   10
  STK19 WILD-TYPE   33  229
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              3              33
  YES            10             229
[1] 2 2
[1] FALSE
D141V11, continuous
D141V12, binary
                 cls
clus                0   1
  STK19 MUTATED     7   6
  STK19 WILD-TYPE  99 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      7    6
  STK19 WILD-TYPE   99  164
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             7              99
  MALE               6             164
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK19 MUTATED       0                         0    13
  STK19 WILD-TYPE     3                         1   259
D141V13, multiclass
                           clus
vv                          STK19 MUTATED STK19 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                13             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"
D141V14, binary
                 cls
clus                0   1
  STK19 MUTATED     0  13
  STK19 WILD-TYPE   3 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0   13
  STK19 WILD-TYPE    3  256
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             256
[1] 2 2
[1] FALSE

Clustering(142) Variable = STK31 MUTATION ANALYSIS
D142V1, survival
                 sevent
clus2               0   1
  STK31 MUTATED    20  14
  STK31 WILD-TYPE 106 126
  STK31 MUTATED STK31 WILD-TYPE 
             34             232 
  STK31 MUTATED STK31 WILD-TYPE 
             14             126 
$`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        62.79        39.62         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 
       49.22        36.30        34.29        30.08        55.69         8.84 
TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3JA 
        9.53        60.49       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-GF-A6C9 TCGA-GN-A266 
        0.99         0.13        11.61        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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       21.44        32.61        25.78        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        60.23         4.34        15.85         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 
       36.85         1.08         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 
        9.99         2.43        32.15        11.31         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       51.12        17.98        60.00        47.21        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-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        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 
      125.65       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 
       53.16        52.67         5.56       122.73        51.62         3.68 
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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       16.14         0.95        18.41        21.73        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74        15.72        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-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        17.33         9.90         7.23         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  STK31 MUTATED STK31 WILD-TYPE 
           0.13            0.16 
  STK31 MUTATED STK31 WILD-TYPE 
         124.31          125.65 
  STK31 MUTATED STK31 WILD-TYPE 
         30.115          15.980 
[1] "0.1 - 124.3 (30.1)" "0.2 - 125.7 (16.0)"
[1] "hr=" "1.5"
D142V2, survival
                 sevent
clus2               0   1
  STK31 MUTATED    21  14
  STK31 WILD-TYPE 108 127
  STK31 MUTATED STK31 WILD-TYPE 
             35             235 
  STK31 MUTATED STK31 WILD-TYPE 
             14             127 
$`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        63.78        56.84 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO 
       17.92       102.90        36.82        67.43        48.72       126.81 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 
       21.67        47.28       134.40       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-GF-A6C9 TCGA-GN-A266 
       27.02        22.92        47.54        11.74        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81        26.89       135.75       178.32        18.18 
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        22.29 
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        68.25        54.02        17.29        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       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       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        64.64         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       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       46.82        39.29        86.14        59.28       314.56       161.03 
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-A2MF TCGA-EE-A2MG 
       28.83        19.76        61.51       103.27       268.73       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       158.63       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       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         3.68        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE 
      172.18       127.20        36.95        34.32       201.80        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19B 
      109.58        35.44        13.94        50.76         9.17        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-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21         6.77        92.98       174.21        15.72       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-A3TV TCGA-FW-A5DY 
       26.73        49.45        77.88         0.20         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 
       64.44        62.79        32.48        39.58         6.67         0.33 
TCGA-RP-A694 
        0.69 

  STK31 MUTATED STK31 WILD-TYPE 
          10.13            0.16 
  STK31 MUTATED STK31 WILD-TYPE 
         151.53          357.37 
  STK31 MUTATED STK31 WILD-TYPE 
          47.54           53.26 
[1] "10.1 - 151.5 (47.5)" "0.2 - 357.4 (53.3)" 
[1] "hr=" "1.1"
D142V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  STK31 MUTATED                    5             0
  STK31 WILD-TYPE                 34             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  STK31 MUTATED                                           5                  25
  STK31 WILD-TYPE                                        55                 146
D142V4, multiclass
                                           clus
vv                                          STK31 MUTATED STK31 WILD-TYPE
  DISTANT METASTASIS                                    5              34
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             5              55
  REGIONAL LYMPH NODE                                  25             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
  STK31 MUTATED             0       1       4        2        4        4
  STK31 WILD-TYPE          10       5      20        8       20       12
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  STK31 MUTATED           0         3         0         4          1          5
  STK31 WILD-TYPE        10        11         9        28         12         18
                 vv
clus              STAGE IIIC STAGE IV
  STK31 MUTATED            2        1
  STK31 WILD-TYPE         44       15
D142V5, multiclass
             clus
vv            STK31 MUTATED STK31 WILD-TYPE
  I OR II NOS             0              10
  STAGE 0                 1               5
  STAGE I                 4              20
  STAGE IA                2               8
  STAGE IB                4              20
  STAGE II                4              12
  STAGE IIA               0              10
  STAGE IIB               3              11
  STAGE IIC               0               9
  STAGE III               4              28
  STAGE IIIA              1              12
  STAGE IIIB              5              18
  STAGE IIIC              2              44
  STAGE IV                1              15
[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    46 50 46 54
D142V6, multiclass
       clus
vv      STK31 MUTATED STK31 WILD-TYPE
  T0+T1             6              46
  T2                9              50
  T3                8              46
  T4                3              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
  STK31 MUTATED    19   5   6   1
  STK31 WILD-TYPE 120  43  27  35
D142V7, multiclass
    clus
vv   STK31 MUTATED STK31 WILD-TYPE
  N0            19             120
  N1             5              43
  N2             6              27
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  STK31 MUTATED    29   1   0   1   0
  STK31 WILD-TYPE 215   3   3   1   8
D142V8, multiclass
     clus
vv    STK31 MUTATED STK31 WILD-TYPE
  M0             29             215
  M1              1               3
  M1A             0               3
  M1B             1               1
  M1C             0               8
[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 87 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED     16    6
  STK31 WILD-TYPE   87   62
     clus
vv    STK31 MUTATED STK31 WILD-TYPE
  NO             16              87
  YES             6              62
[1] 2 2
[1] FALSE
D142V10, binary
                 cls
clus                0   1
  STK31 MUTATED     8  27
  STK31 WILD-TYPE  28 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED      8   27
  STK31 WILD-TYPE   28  212
     clus
vv    STK31 MUTATED STK31 WILD-TYPE
  NO              8              28
  YES            27             212
[1] 2 2
[1] FALSE
D142V11, continuous
D142V12, binary
                 cls
clus                0   1
  STK31 MUTATED    10  25
  STK31 WILD-TYPE  96 145
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED     10   25
  STK31 WILD-TYPE   96  145
        clus
vv       STK31 MUTATED STK31 WILD-TYPE
  FEMALE            10              96
  MALE              25             145
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK31 MUTATED       0                         0    35
  STK31 WILD-TYPE     3                         1   237
D142V13, multiclass
                           clus
vv                          STK31 MUTATED STK31 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                35             237
[1] 3 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  34
  STK31 WILD-TYPE   2 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED      1   34
  STK31 WILD-TYPE    2  235
                        clus
vv                       STK31 MUTATED STK31 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            34             235
[1] 2 2
[1] FALSE

Clustering(143) Variable = ROS1 MUTATION ANALYSIS
D143V1, survival
                sevent
clus2              0   1
  ROS1 MUTATED    29  25
  ROS1 WILD-TYPE  97 115
  ROS1 MUTATED ROS1 WILD-TYPE 
            54            212 
  ROS1 MUTATED ROS1 WILD-TYPE 
            25            115 
$`ROS1 MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JP TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T 
       28.08        59.57       103.59        26.37        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I7 
       52.01        13.68         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        15.85        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GC 
       62.79         1.08         2.43        32.15        36.30        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        55.69         1.15         9.53 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 
       63.42        53.16        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-GF-A6C9 TCGA-GN-A266 TCGA-QB-A6FS TCGA-RP-A694 
        6.41         0.99        11.61        10.13         5.79         0.69 

$`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        86.76        11.41        44.19 
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        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GO 
       54.74        31.30        54.31        32.28        21.44        47.87 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW 
       17.72        23.11        21.93         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        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.35        13.22        11.57        10.55         6.31         8.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I 
       12.20         4.31        60.23         4.34         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        7.99         9.90         8.55        36.85        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.09         8.84         9.99         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        36.33        51.12        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       47.21        16.01        35.54        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-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       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 
       60.49        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA 
        3.68        30.15        13.81         3.22        22.92        22.22 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        0.95        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       12.95        38.40         5.72        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       11.90        11.11        34.88         4.21        13.45        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        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-ER-A42K TCGA-FR-A69P 
        9.04         6.58        22.49         1.71         5.62        15.72 
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-A1ZG 
        7.33         3.39        20.38         8.22        19.53         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       30.87        12.92        12.89        47.38        52.08         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        17.33         9.90         7.23         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-RP-A693 
       14.70         0.33 

  ROS1 MUTATED ROS1 WILD-TYPE 
          0.69           0.13 
  ROS1 MUTATED ROS1 WILD-TYPE 
        114.15         125.65 
  ROS1 MUTATED ROS1 WILD-TYPE 
        18.920         16.355 
[1] "0.7 - 114.2 (18.9)" "0.1 - 125.7 (16.4)"
[1] "hr=" "1.1"
D143V2, survival
                sevent
clus2              0   1
  ROS1 MUTATED    29  25
  ROS1 WILD-TYPE 100 116
  ROS1 MUTATED ROS1 WILD-TYPE 
            54            216 
  ROS1 MUTATED ROS1 WILD-TYPE 
            25            116 
$`ROS1 MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JP TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T 
       28.08        59.57       103.59        39.75        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I7 
      135.75       178.32        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        91.56        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GC 
       63.78         2.60        25.87       195.02        36.82        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       126.81        14.30        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 
       96.23       162.48        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-GF-A6C9 TCGA-GN-A266 TCGA-QB-A6FS TCGA-RP-A694 
       49.45        22.92        11.74        10.13         6.67         0.69 

$`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        86.76        11.87        62.07 
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        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GO 
       55.73        56.35       145.12        32.94        22.62       137.92 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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 
       22.29         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        68.25        54.02        17.29        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 
      133.81       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        64.64        56.84        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 
       86.14        59.28       314.56       161.03       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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       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       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
       13.81       172.18       127.20        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       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-ER-A42K TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       46.98        33.21         6.77        15.72       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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        40.27         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26        74.73        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       26.56        49.48        27.09        77.82        66.67       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-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         7.23         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 
       84.72        64.44        62.79        32.48        39.58         0.33 

  ROS1 MUTATED ROS1 WILD-TYPE 
          0.69           0.16 
  ROS1 MUTATED ROS1 WILD-TYPE 
        268.93         357.37 
  ROS1 MUTATED ROS1 WILD-TYPE 
        48.805         53.225 
[1] "0.7 - 268.9 (48.8)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1"  
D143V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  ROS1 MUTATED                    9             1
  ROS1 WILD-TYPE                 30             4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ROS1 MUTATED                                          13                  33
  ROS1 WILD-TYPE                                        47                 138
D143V4, multiclass
                                           clus
vv                                          ROS1 MUTATED ROS1 WILD-TYPE
  DISTANT METASTASIS                                   9             30
  PRIMARY TUMOR                                        1              4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE           13             47
  REGIONAL LYMPH NODE                                 33            138
[1] 4 2
[1] 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      20        8       19        9
                vv
clus             STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ROS1 MUTATED           2         2         2         7          3          6
  ROS1 WILD-TYPE         8        12         7        25         10         17
                vv
clus             STAGE IIIC STAGE IV
  ROS1 MUTATED            9        2
  ROS1 WILD-TYPE         37       14
D143V5, multiclass
             clus
vv            ROS1 MUTATED ROS1 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                2              4
  STAGE I                4             20
  STAGE IA               2              8
  STAGE IB               5             19
  STAGE II               7              9
  STAGE IIA              2              8
  STAGE IIB              2             12
  STAGE IIC              2              7
  STAGE III              7             25
  STAGE IIIA             3             10
  STAGE IIIB             6             17
  STAGE IIIC             9             37
  STAGE IV               2             14
[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    40 51 38 46
D143V6, multiclass
       clus
vv      ROS1 MUTATED ROS1 WILD-TYPE
  T0+T1           12             40
  T2               8             51
  T3              16             38
  T4              11             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
  ROS1 MUTATED    28  12   7   5
  ROS1 WILD-TYPE 111  36  26  31
D143V7, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  N0           28            111
  N1           12             36
  N2            7             26
  N3            5             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
  ROS1 MUTATED    52   0   0   1   1
  ROS1 WILD-TYPE 192   4   3   1   7
D143V8, multiclass
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  M0            52            192
  M1             0              4
  M1A            0              3
  M1B            1              1
  M1C            1              7
[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 82 55
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     21   13
  ROS1 WILD-TYPE   82   55
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  NO            21             82
  YES           13             55
[1] 2 2
[1] FALSE
D143V10, binary
                cls
clus               0   1
  ROS1 MUTATED    11  45
  ROS1 WILD-TYPE  25 194
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     11   45
  ROS1 WILD-TYPE   25  194
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  NO            11             25
  YES           45            194
[1] 2 2
[1] FALSE
D143V11, continuous
D143V12, binary
                cls
clus               0   1
  ROS1 MUTATED    16  40
  ROS1 WILD-TYPE  90 130
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     16   40
  ROS1 WILD-TYPE   90  130
        clus
vv       ROS1 MUTATED ROS1 WILD-TYPE
  FEMALE           16             90
  MALE             40            130
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ROS1 MUTATED       0                         0    56
  ROS1 WILD-TYPE     3                         1   216
D143V13, multiclass
                           clus
vv                          ROS1 MUTATED ROS1 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               56            216
[1] 3 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  55
  ROS1 WILD-TYPE   2 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED      1   55
  ROS1 WILD-TYPE    2  214
                        clus
vv                       ROS1 MUTATED ROS1 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           55            214
[1] 2 2
[1] FALSE

Clustering(144) Variable = KCNB2 MUTATION ANALYSIS
D144V1, survival
                 sevent
clus2               0   1
  KCNB2 MUTATED    23  33
  KCNB2 WILD-TYPE 103 107
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             56             210 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             33             107 
$`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 
       29.23        32.61        25.78        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        62.79         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 
       55.69         9.53        63.42        60.49        53.16         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         0.85 
TCGA-GF-A6C9 TCGA-GN-A266 
       11.61        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        86.76        44.19         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        59.57       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        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.28        21.44        52.01        47.87        13.68        17.72 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        13.22 
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        60.23 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
       15.85         9.21         1.18         7.99         9.90         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         1.08        39.62        12.03         8.09         8.84 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       32.15         8.09        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       51.12        34.29        60.00        47.21        19.43        16.01 
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-A2ME 
        8.84        98.27         2.70         6.18        47.51        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73        44.25         7.96        14.56       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA 
       56.02        25.08        26.99        21.60        52.67       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73        51.62        15.95         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22         0.95        18.41        21.73        33.60 
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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       13.45        42.84        34.68         9.57        36.07         6.58 
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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 
        5.62        85.74        15.72        64.47         3.45        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       15.52         7.33         3.39         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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         7.23        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.42        12.16        14.70         5.79         0.33         0.69 

  KCNB2 MUTATED KCNB2 WILD-TYPE 
           0.85            0.13 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
          92.42          125.65 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
         16.405          16.900 
[1] "0.8 - 92.4 (16.4)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.2"
D144V2, survival
                 sevent
clus2               0   1
  KCNB2 MUTATED    24  33
  KCNB2 WILD-TYPE 105 108
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             57             213 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
             33             108 
$`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 
       45.30        63.81        26.89       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        63.78        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       126.81        47.28        96.23       134.40       162.48 
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-GF-A6C9 TCGA-GN-A266 
        2.04        11.74        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        86.76        62.07       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        59.57       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       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62       135.75       137.92       178.32        18.18 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      151.53        54.67         6.41        22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 
       54.02        17.29        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       133.81        91.56       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        64.64         2.60        56.84 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       56.42        37.35        14.47       195.02        17.92       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       36.82        39.29        86.14        59.28        67.43       161.03 
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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG 
       43.23        71.21       124.31       122.73        51.62        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       109.58       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-A19N TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       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-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21         6.77       174.21        15.72 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      216.92        48.59        20.91        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-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26        74.73        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
       47.54         0.16        19.30         9.90         7.23       139.89 
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 TCGA-RP-A693 TCGA-RP-A694 
        6.67         0.33         0.69 

  KCNB2 MUTATED KCNB2 WILD-TYPE 
           2.04            0.16 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
         357.37          268.93 
  KCNB2 MUTATED KCNB2 WILD-TYPE 
          47.84           53.19 
[1] "2.0 - 357.4 (47.8)" "0.2 - 268.9 (53.2)"
[1] "hr=" "1.1"
D144V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  KCNB2 MUTATED                   11             1
  KCNB2 WILD-TYPE                 28             4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  KCNB2 MUTATED                                          12                  34
  KCNB2 WILD-TYPE                                        48                 137
D144V4, multiclass
                                           clus
vv                                          KCNB2 MUTATED KCNB2 WILD-TYPE
  DISTANT METASTASIS                                   11              28
  PRIMARY TUMOR                                         1               4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            12              48
  REGIONAL LYMPH NODE                                  34             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
  KCNB2 MUTATED             5       1       1        5        5        5
  KCNB2 WILD-TYPE           5       5      23        5       19       11
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KCNB2 MUTATED           5         4         1         6          1          7
  KCNB2 WILD-TYPE         5        10         8        26         12         16
                 vv
clus              STAGE IIIC STAGE IV
  KCNB2 MUTATED            8        1
  KCNB2 WILD-TYPE         38       15
D144V5, multiclass
             clus
vv            KCNB2 MUTATED KCNB2 WILD-TYPE
  I OR II NOS             5               5
  STAGE 0                 1               5
  STAGE I                 1              23
  STAGE IA                5               5
  STAGE IB                5              19
  STAGE II                5              11
  STAGE IIA               5               5
  STAGE IIB               4              10
  STAGE IIC               1               8
  STAGE III               6              26
  STAGE IIIA              1              12
  STAGE IIIB              7              16
  STAGE IIIC              8              38
  STAGE IV                1              15
[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    43 50 36 46
D144V6, multiclass
       clus
vv      KCNB2 MUTATED KCNB2 WILD-TYPE
  T0+T1             9              43
  T2                9              50
  T3               18              36
  T4               11              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
  KCNB2 MUTATED    32  11   7   4
  KCNB2 WILD-TYPE 107  37  26  32
D144V7, multiclass
    clus
vv   KCNB2 MUTATED KCNB2 WILD-TYPE
  N0            32             107
  N1            11              37
  N2             7              26
  N3             4              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
  KCNB2 MUTATED    55   0   1   0   0
  KCNB2 WILD-TYPE 189   4   2   2   8
D144V8, multiclass
     clus
vv    KCNB2 MUTATED KCNB2 WILD-TYPE
  M0             55             189
  M1              0               4
  M1A             1               2
  M1B             0               2
  M1C             0               8
[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 77 51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED     26   17
  KCNB2 WILD-TYPE   77   51
     clus
vv    KCNB2 MUTATED KCNB2 WILD-TYPE
  NO             26              77
  YES            17              51
[1] 2 2
[1] FALSE
D144V10, binary
                 cls
clus                0   1
  KCNB2 MUTATED     5  53
  KCNB2 WILD-TYPE  31 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED      5   53
  KCNB2 WILD-TYPE   31  186
     clus
vv    KCNB2 MUTATED KCNB2 WILD-TYPE
  NO              5              31
  YES            53             186
[1] 2 2
[1] FALSE
D144V11, continuous
D144V12, binary
                 cls
clus                0   1
  KCNB2 MUTATED    20  38
  KCNB2 WILD-TYPE  86 132
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED     20   38
  KCNB2 WILD-TYPE   86  132
        clus
vv       KCNB2 MUTATED KCNB2 WILD-TYPE
  FEMALE            20              86
  MALE              38             132
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNB2 MUTATED       1                         0    57
  KCNB2 WILD-TYPE     2                         1   215
D144V13, multiclass
                           clus
vv                          KCNB2 MUTATED KCNB2 WILD-TYPE
  ASIAN                                 1               2
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                57             215
[1] 3 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  55
  KCNB2 WILD-TYPE   2 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB2 MUTATED      1   55
  KCNB2 WILD-TYPE    2  214
                        clus
vv                       KCNB2 MUTATED KCNB2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            55             214
[1] 2 2
[1] FALSE

Clustering(145) Variable = ART3 MUTATION ANALYSIS
D145V1, survival
                sevent
clus2              0   1
  ART3 MUTATED     5   7
  ART3 WILD-TYPE 121 133
  ART3 MUTATED ART3 WILD-TYPE 
            12            254 
  ART3 MUTATED ART3 WILD-TYPE 
             7            133 
$`ART3 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-EE-A2A6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A3AG 
       46.98        82.29        36.33         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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         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        59.57       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 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85 
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 
       62.79         8.55        36.85         1.08        39.62         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        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30         9.67        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        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        55.69         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-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       125.65       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        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        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-A19Q TCGA-ER-A19S 
        4.21        13.45        28.60        42.84         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
        1.71         5.62        18.41        85.74        15.72        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-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        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ART3 MUTATED ART3 WILD-TYPE 
          0.99           0.13 
  ART3 MUTATED ART3 WILD-TYPE 
         82.29         125.65 
  ART3 MUTATED ART3 WILD-TYPE 
        23.675         16.900 
[1] "1.0 - 82.3 (23.7)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.1"
D145V2, survival
                sevent
clus2              0   1
  ART3 MUTATED     5   7
  ART3 WILD-TYPE 124 134
  ART3 MUTATED ART3 WILD-TYPE 
            12            258 
  ART3 MUTATED ART3 WILD-TYPE 
             7            134 
$`ART3 MUTATED`
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-EE-A2A6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A3AG 
       46.98       166.52        86.14        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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       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        59.57       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 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       18.18       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        22.29         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 
       68.25        54.02        17.29        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       133.81       151.27        91.56       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        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        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       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        36.82        39.29        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       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 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       109.58       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-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.05        50.89        37.25         8.88       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-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       92.98       174.21        15.72       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-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        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       64.44        62.79        39.58         6.67         0.33         0.69 

  ART3 MUTATED ART3 WILD-TYPE 
         22.92           0.16 
  ART3 MUTATED ART3 WILD-TYPE 
        166.52         357.37 
  ART3 MUTATED ART3 WILD-TYPE 
        47.130         53.175 
[1] "22.9 - 166.5 (47.1)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "1.3"
D145V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  ART3 MUTATED                    1             0
  ART3 WILD-TYPE                 38             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  ART3 MUTATED                                           3                   8
  ART3 WILD-TYPE                                        57                 163
D145V4, multiclass
                                           clus
vv                                          ART3 MUTATED ART3 WILD-TYPE
  DISTANT METASTASIS                                   1             38
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             57
  REGIONAL LYMPH NODE                                  8            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
  ART3 MUTATED             1       0       0        1        0        1
  ART3 WILD-TYPE           9       6      24        9       24       15
                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        28         12         23
                vv
clus             STAGE IIIC STAGE IV
  ART3 MUTATED            0        0
  ART3 WILD-TYPE         46       16
D145V5, multiclass
             clus
vv            ART3 MUTATED ART3 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                0              6
  STAGE I                0             24
  STAGE IA               1              9
  STAGE IB               0             24
  STAGE II               1             15
  STAGE IIA              1              9
  STAGE IIB              2             12
  STAGE IIC              0              9
  STAGE III              4             28
  STAGE IIIA             1             12
  STAGE IIIB             0             23
  STAGE IIIC             0             46
  STAGE IV               0             16
[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    49 58 49 56
D145V6, multiclass
       clus
vv      ART3 MUTATED ART3 WILD-TYPE
  T0+T1            3             49
  T2               1             58
  T3               5             49
  T4               1             56
[1] 4 2
[1] TRUE
[1] "dimension of 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 131  46  31  36
D145V7, multiclass
    clus
vv   ART3 MUTATED ART3 WILD-TYPE
  N0            8            131
  N1            2             46
  N2            2             31
  N3            0             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              M0  M1 M1A M1B M1C
  ART3 MUTATED    12   0   0   0   0
  ART3 WILD-TYPE 232   4   3   2   8
D145V8, multiclass
     clus
vv    ART3 MUTATED ART3 WILD-TYPE
  M0            12            232
  M1             0              4
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 98 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      5    2
  ART3 WILD-TYPE   98   66
     clus
vv    ART3 MUTATED ART3 WILD-TYPE
  NO             5             98
  YES            2             66
[1] 2 2
[1] FALSE
D145V10, binary
                cls
clus               0   1
  ART3 MUTATED     2  10
  ART3 WILD-TYPE  34 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      2   10
  ART3 WILD-TYPE   34  229
     clus
vv    ART3 MUTATED ART3 WILD-TYPE
  NO             2             34
  YES           10            229
[1] 2 2
[1] FALSE
D145V11, continuous
D145V12, binary
                cls
clus               0   1
  ART3 MUTATED     5   7
  ART3 WILD-TYPE 101 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      5    7
  ART3 WILD-TYPE  101  163
        clus
vv       ART3 MUTATED ART3 WILD-TYPE
  FEMALE            5            101
  MALE              7            163
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ART3 MUTATED       0                         0    12
  ART3 WILD-TYPE     3                         1   260
D145V13, multiclass
                           clus
vv                          ART3 MUTATED ART3 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               12            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"
D145V14, binary
                cls
clus               0   1
  ART3 MUTATED     1  11
  ART3 WILD-TYPE   2 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART3 MUTATED      1   11
  ART3 WILD-TYPE    2  258
                        clus
vv                       ART3 MUTATED ART3 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           11            258
[1] 2 2
[1] FALSE

Clustering(146) Variable = CLDN4 MUTATION ANALYSIS
D146V1, survival
                 sevent
clus2               0   1
  CLDN4 MUTATED     6   4
  CLDN4 WILD-TYPE 120 136
  CLDN4 MUTATED CLDN4 WILD-TYPE 
             10             256 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
              4             136 
$`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 TCGA-GF-A6C9 
       53.16         7.30         0.99        11.61 

$`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        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         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 
       59.57       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        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       13.68        17.72        23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN 
       13.15         0.20        23.15        19.00        13.35        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        60.23         4.34        15.85         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        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         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        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        33.83        55.69         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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        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       125.65       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        60.49        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         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-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
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-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        17.33         9.90         7.23         0.85        44.28 
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 TCGA-RP-A693 TCGA-RP-A694 
       14.70         5.79         0.33         0.69 

  CLDN4 MUTATED CLDN4 WILD-TYPE 
           0.99            0.13 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
          53.16          125.65 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
          19.96           16.90 
[1] "1.0 - 53.2 (20.0)"  "0.1 - 125.7 (16.9)"
[1] "hr=" "1.2"
D146V2, survival
                 sevent
clus2               0   1
  CLDN4 MUTATED     6   4
  CLDN4 WILD-TYPE 123 137
  CLDN4 MUTATED CLDN4 WILD-TYPE 
             10             260 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
              4             137 
$`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 TCGA-GF-A6C9 
      162.48        27.72        22.92        11.74 

$`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        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       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 
       59.57       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        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      178.32        18.18       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        22.29         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 
       68.25        54.02        17.29        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 
      133.81       151.27        91.56       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        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       56.84        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       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
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 
      126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
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       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         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-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
        6.77        92.98       174.21        15.72       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        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       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 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CLDN4 MUTATED CLDN4 WILD-TYPE 
          11.74            0.16 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
         194.83          357.37 
  CLDN4 MUTATED CLDN4 WILD-TYPE 
         37.905          52.585 
[1] "11.7 - 194.8 (37.9)" "0.2 - 357.4 (52.6)" 
[1] "hr=" "1.2"
D146V3, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CLDN4 MUTATED                    2             0
  CLDN4 WILD-TYPE                 37             5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  CLDN4 MUTATED                                           3                   6
  CLDN4 WILD-TYPE                                        57                 165
D146V4, multiclass
                                           clus
vv                                          CLDN4 MUTATED CLDN4 WILD-TYPE
  DISTANT METASTASIS                                    2              37
  PRIMARY TUMOR                                         0               5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE             3              57
  REGIONAL LYMPH NODE                                   6             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
  CLDN4 MUTATED             1       0       1        0        1        2
  CLDN4 WILD-TYPE           9       6      23       10       23       14
                 vv
clus              STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CLDN4 MUTATED           0         0         1         1          0          2
  CLDN4 WILD-TYPE        10        14         8        31         13         21
                 vv
clus              STAGE IIIC STAGE IV
  CLDN4 MUTATED            2        0
  CLDN4 WILD-TYPE         44       16
D146V5, multiclass
             clus
vv            CLDN4 MUTATED CLDN4 WILD-TYPE
  I OR II NOS             1               9
  STAGE 0                 0               6
  STAGE I                 1              23
  STAGE IA                0              10
  STAGE IB                1              23
  STAGE II                2              14
  STAGE IIA               0              10
  STAGE IIB               0              14
  STAGE IIC               1               8
  STAGE III               1              31
  STAGE IIIA              0              13
  STAGE IIIB              2              21
  STAGE IIIC              2              44
  STAGE IV                0              16
[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    50 58 51 55
D146V6, multiclass
       clus
vv      CLDN4 MUTATED CLDN4 WILD-TYPE
  T0+T1             2              50
  T2                1              58
  T3                3              51
  T4                2              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
  CLDN4 MUTATED     6   1   2   1
  CLDN4 WILD-TYPE 133  47  31  35
D146V7, multiclass
    clus
vv   CLDN4 MUTATED CLDN4 WILD-TYPE
  N0             6             133
  N1             1              47
  N2             2              31
  N3             1              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               M0  M1 M1A M1B M1C
  CLDN4 MUTATED    10   0   0   0   0
  CLDN4 WILD-TYPE 234   4   3   2   8
D146V8, multiclass
     clus
vv    CLDN4 MUTATED CLDN4 WILD-TYPE
  M0             10             234
  M1              0               4
  M1A             0               3
  M1B             0               2
  M1C             0               8
[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 100  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      3    3
  CLDN4 WILD-TYPE  100   65
     clus
vv    CLDN4 MUTATED CLDN4 WILD-TYPE
  NO              3             100
  YES             3              65
[1] 2 2
[1] FALSE
D146V10, binary
                 cls
clus                0   1
  CLDN4 MUTATED     2   9
  CLDN4 WILD-TYPE  34 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      2    9
  CLDN4 WILD-TYPE   34  230
     clus
vv    CLDN4 MUTATED CLDN4 WILD-TYPE
  NO              2              34
  YES             9             230
[1] 2 2
[1] FALSE
D146V11, continuous
D146V12, binary
                 cls
clus                0   1
  CLDN4 MUTATED     3   8
  CLDN4 WILD-TYPE 103 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      3    8
  CLDN4 WILD-TYPE  103  162
        clus
vv       CLDN4 MUTATED CLDN4 WILD-TYPE
  FEMALE             3             103
  MALE               8             162
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLDN4 MUTATED       0                         0    11
  CLDN4 WILD-TYPE     3                         1   261
D146V13, multiclass
                           clus
vv                          CLDN4 MUTATED CLDN4 WILD-TYPE
  ASIAN                                 0               3
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             261
[1] 3 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  11
  CLDN4 WILD-TYPE   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN4 MUTATED      0   11
  CLDN4 WILD-TYPE    3  258
                        clus
vv                       CLDN4 MUTATED CLDN4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             258
[1] 2 2
[1] FALSE

Clustering(147) Variable = RAG2 MUTATION ANALYSIS
D147V1, survival
                sevent
clus2              0   1
  RAG2 MUTATED     8  10
  RAG2 WILD-TYPE 118 130
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            248 
  RAG2 MUTATED RAG2 WILD-TYPE 
            10            130 
$`RAG2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JF TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       70.16       110.79        44.19         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        60.00         5.42        63.42        60.49        15.95 
TCGA-EE-A3JD TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-GF-A3OT TCGA-QB-A6FS 
       27.35        15.72        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        86.76        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        59.57       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        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01        21.93         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-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
        0.20        23.15        19.00        13.35        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        60.23        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        7.99        11.15        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       39.62         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 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI 
       36.33        51.12        34.29        17.98        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        55.69 
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-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56       125.65       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        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22         0.95        18.41        21.73        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-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       22.49         1.71         5.62        18.41        85.74        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-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-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-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       17.33         7.23         0.85        11.61        44.28        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-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  RAG2 MUTATED RAG2 WILD-TYPE 
          4.34           0.13 
  RAG2 MUTATED RAG2 WILD-TYPE 
        110.79         125.65 
  RAG2 MUTATED RAG2 WILD-TYPE 
        18.165         16.900 
[1] "4.3 - 110.8 (18.2)" "0.1 - 125.7 (16.9)"
[1] "hr=" "1.1"
D147V2, survival
                sevent
clus2              0   1
  RAG2 MUTATED     8  10
  RAG2 WILD-TYPE 121 131
  RAG2 MUTATED RAG2 WILD-TYPE 
            18            252 
  RAG2 MUTATED RAG2 WILD-TYPE 
            10            131 
$`RAG2 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JF TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       71.80       133.25        62.07       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       161.03        13.91        96.23       134.40        23.47 
TCGA-EE-A3JD TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-GF-A3OT TCGA-QB-A6FS 
       27.35        15.72        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        86.76        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        59.57       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        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       135.75       137.92       178.32        18.18 
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 
       22.29         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        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       54.02        17.29        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 
      133.81        91.56       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 
       63.78        72.07        64.64         2.60        56.84        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       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
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       126.81        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-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       158.63       203.05       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       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         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-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       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-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
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-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6.77        92.98       174.21       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
      202.65        28.08         7.79        27.72        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-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        19.30         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-RP-A693 TCGA-RP-A694 
       64.44        62.79        32.48        39.58         0.33         0.69 

  RAG2 MUTATED RAG2 WILD-TYPE 
          6.67           0.16 
  RAG2 MUTATED RAG2 WILD-TYPE 
        357.37         314.56 
  RAG2 MUTATED RAG2 WILD-TYPE 
        58.995         51.485 
[1] "6.7 - 357.4 (59.0)" "0.2 - 314.6 (51.5)"
[1] "hr=" "1.2"
D147V3, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  RAG2 MUTATED                    5             0
  RAG2 WILD-TYPE                 34             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  RAG2 MUTATED                                           3                  10
  RAG2 WILD-TYPE                                        57                 161
D147V4, multiclass
                                           clus
vv                                          RAG2 MUTATED RAG2 WILD-TYPE
  DISTANT METASTASIS                                   5             34
  PRIMARY TUMOR                                        0              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE            3             57
  REGIONAL LYMPH NODE                                 10            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
  RAG2 MUTATED             1       1       2        1        2        0
  RAG2 WILD-TYPE           9       5      22        9       22       16
                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        28         13         22
                vv
clus             STAGE IIIC STAGE IV
  RAG2 MUTATED            3        1
  RAG2 WILD-TYPE         43       15
D147V5, multiclass
             clus
vv            RAG2 MUTATED RAG2 WILD-TYPE
  I OR II NOS            1              9
  STAGE 0                1              5
  STAGE I                2             22
  STAGE IA               1              9
  STAGE IB               2             22
  STAGE II               0             16
  STAGE IIA              1              9
  STAGE IIB              1             13
  STAGE IIC              0              9
  STAGE III              4             28
  STAGE IIIA             0             13
  STAGE IIIB             1             22
  STAGE IIIC             3             43
  STAGE IV               1             15
[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    48 56 51 54
D147V6, multiclass
       clus
vv      RAG2 MUTATED RAG2 WILD-TYPE
  T0+T1            4             48
  T2               3             56
  T3               3             51
  T4               3             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
  RAG2 MUTATED    11   2   2   3
  RAG2 WILD-TYPE 128  46  31  33
D147V7, multiclass
    clus
vv   RAG2 MUTATED RAG2 WILD-TYPE
  N0           11            128
  N1            2             46
  N2            2             31
  N3            3             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
  RAG2 MUTATED    16   1   0   0   0
  RAG2 WILD-TYPE 228   3   3   2   8
D147V8, multiclass
     clus
vv    RAG2 MUTATED RAG2 WILD-TYPE
  M0            16            228
  M1             1              3
  M1A            0              3
  M1B            0              2
  M1C            0              8
[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 96 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      7    2
  RAG2 WILD-TYPE   96   66
     clus
vv    RAG2 MUTATED RAG2 WILD-TYPE
  NO             7             96
  YES            2             66
[1] 2 2
[1] FALSE
D147V10, binary
                cls
clus               0   1
  RAG2 MUTATED     5  13
  RAG2 WILD-TYPE  31 226
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      5   13
  RAG2 WILD-TYPE   31  226
     clus
vv    RAG2 MUTATED RAG2 WILD-TYPE
  NO             5             31
  YES           13            226
[1] 2 2
[1] FALSE
D147V11, continuous
D147V12, binary
                cls
clus               0   1
  RAG2 MUTATED     4  14
  RAG2 WILD-TYPE 102 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      4   14
  RAG2 WILD-TYPE  102  156
        clus
vv       RAG2 MUTATED RAG2 WILD-TYPE
  FEMALE            4            102
  MALE             14            156
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAG2 MUTATED       0                         0    18
  RAG2 WILD-TYPE     3                         1   254
D147V13, multiclass
                           clus
vv                          RAG2 MUTATED RAG2 WILD-TYPE
  ASIAN                                0              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               18            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"
D147V14, binary
                cls
clus               0   1
  RAG2 MUTATED     0  18
  RAG2 WILD-TYPE   3 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG2 MUTATED      0   18
  RAG2 WILD-TYPE    3  251
                        clus
vv                       RAG2 MUTATED RAG2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           18            251
[1] 2 2
[1] FALSE
