[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/22507034/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/22813361/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=290, common to both=290
[1] 117 290
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            87            203 
  NRAS MUTATED NRAS WILD-TYPE 
            87            203 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            48            242 
  TP53 MUTATED TP53 WILD-TYPE 
            48            242 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              41              249 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              41              249 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           38           252 
  NF1 MUTATED NF1 WILD-TYPE 
           38           252 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            25            265 
  PTEN MUTATED PTEN WILD-TYPE 
            25            265 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            270 
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            270 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             37             253 
  ARID2 MUTATED ARID2 WILD-TYPE 
             37             253 
[1] "C15ORF23 MUTATION ANALYSIS"
[1] 3
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                19                271 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                19                271 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               8              282 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               8              282 
[1] "ZFX MUTATION ANALYSIS"
[1] 3
  ZFX MUTATED ZFX WILD-TYPE 
           15           275 
  ZFX MUTATED ZFX WILD-TYPE 
           15           275 
[1] "SLC38A4 MUTATION ANALYSIS"
[1] 3
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               33               257 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               33               257 
[1] "FAM58A MUTATION ANALYSIS"
[1] 3
  FAM58A MUTATED FAM58A WILD-TYPE 
               6              284 
  FAM58A MUTATED FAM58A WILD-TYPE 
               6              284 
[1] "PPP6C MUTATION ANALYSIS"
[1] 3
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             270 
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             270 
[1] "C7ORF58 MUTATION ANALYSIS"
[1] 3
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               37               253 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               37               253 
[1] "COL3A1 MUTATION ANALYSIS"
[1] 3
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              59              231 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              59              231 
[1] "CDK4 MUTATION ANALYSIS"
[1] 3
  CDK4 MUTATED CDK4 WILD-TYPE 
             8            282 
  CDK4 MUTATED CDK4 WILD-TYPE 
             8            282 
[1] "DSG3 MUTATION ANALYSIS"
[1] 3
  DSG3 MUTATED DSG3 WILD-TYPE 
            48            242 
  DSG3 MUTATED DSG3 WILD-TYPE 
            48            242 
[1] "MLL MUTATION ANALYSIS"
[1] 3
  MLL MUTATED MLL WILD-TYPE 
           40           250 
  MLL MUTATED MLL WILD-TYPE 
           40           250 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
             20             270 
  DDX3X MUTATED DDX3X WILD-TYPE 
             20             270 
[1] "HSD11B1 MUTATION ANALYSIS"
[1] 3
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               276 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               276 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             47             243 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             47             243 
[1] "ATP5F1 MUTATION ANALYSIS"
[1] 3
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               6              284 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               6              284 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
            42            248 
  RPTN MUTATED RPTN WILD-TYPE 
            42            248 
[1] "KRTAP5-10 MUTATION ANALYSIS"
[1] 3
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                 10                 280 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                 10                 280 
[1] "GML MUTATION ANALYSIS"
[1] 3
  GML MUTATED GML WILD-TYPE 
           11           279 
  GML MUTATED GML WILD-TYPE 
           11           279 
[1] "MAP2K1 MUTATION ANALYSIS"
[1] 3
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              15              275 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              15              275 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            15            275 
  IDH1 MUTATED IDH1 WILD-TYPE 
            15            275 
[1] "KEL MUTATION ANALYSIS"
[1] 3
  KEL MUTATED KEL WILD-TYPE 
           36           254 
  KEL MUTATED KEL WILD-TYPE 
           36           254 
[1] "RQCD1 MUTATION ANALYSIS"
[1] 3
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              9             281 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              9             281 
[1] "NGF MUTATION ANALYSIS"
[1] 3
  NGF MUTATED NGF WILD-TYPE 
            9           281 
  NGF MUTATED NGF WILD-TYPE 
            9           281 
[1] "DMC1 MUTATION ANALYSIS"
[1] 3
  DMC1 MUTATED DMC1 WILD-TYPE 
            11            279 
  DMC1 MUTATED DMC1 WILD-TYPE 
            11            279 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              26              264 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              26              264 
[1] "CYP3A5 MUTATION ANALYSIS"
[1] 3
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
              13              277 
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
              13              277 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           145            145 
  BRAF MUTATED BRAF WILD-TYPE 
           145            145 
[1] "NBPF1 MUTATION ANALYSIS"
[1] 3
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             26             264 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             26             264 
[1] "ZNF780B MUTATION ANALYSIS"
[1] 3
  ZNF780B MUTATED ZNF780B WILD-TYPE 
               10               280 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
               10               280 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
             14             276 
  STK19 MUTATED STK19 WILD-TYPE 
             14             276 
[1] "KYNU MUTATION ANALYSIS"
[1] 3
  KYNU MUTATED KYNU WILD-TYPE 
            16            274 
  KYNU MUTATED KYNU WILD-TYPE 
            16            274 
[1] "ANO4 MUTATION ANALYSIS"
[1] 3
  ANO4 MUTATED ANO4 WILD-TYPE 
            46            244 
  ANO4 MUTATED ANO4 WILD-TYPE 
            46            244 
[1] "SLC27A5 MUTATION ANALYSIS"
[1] 3
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
               10               280 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
               10               280 
[1] "POTEG MUTATION ANALYSIS"
[1] 3
  POTEG MUTATED POTEG WILD-TYPE 
             27             263 
  POTEG MUTATED POTEG WILD-TYPE 
             27             263 
[1] "TPTE MUTATION ANALYSIS"
[1] 3
  TPTE MUTATED TPTE WILD-TYPE 
            64            226 
  TPTE MUTATED TPTE WILD-TYPE 
            64            226 
[1] "USH2A MUTATION ANALYSIS"
[1] 3
  USH2A MUTATED USH2A WILD-TYPE 
             91             199 
  USH2A MUTATED USH2A WILD-TYPE 
             91             199 
[1] "XIRP2 MUTATION ANALYSIS"
[1] 3
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             98             192 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             98             192 
[1] "THSD7B MUTATION ANALYSIS"
[1] 3
  THSD7B MUTATED THSD7B WILD-TYPE 
              92              198 
  THSD7B MUTATED THSD7B WILD-TYPE 
              92              198 
[1] "USP17L2 MUTATION ANALYSIS"
[1] 3
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               22               268 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               22               268 
[1] "S100A8 MUTATION ANALYSIS"
[1] 3
  S100A8 MUTATED S100A8 WILD-TYPE 
               8              282 
  S100A8 MUTATED S100A8 WILD-TYPE 
               8              282 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              16              274 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              16              274 
[1] "USP9X MUTATION ANALYSIS"
[1] 3
  USP9X MUTATED USP9X WILD-TYPE 
             17             273 
  USP9X MUTATED USP9X WILD-TYPE 
             17             273 
[1] "C10ORF28 MUTATION ANALYSIS"
[1] 3
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 7                283 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 7                283 
[1] "MAN1A1 MUTATION ANALYSIS"
[1] 3
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              15              275 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              15              275 
[1] "OXA1L MUTATION ANALYSIS"
[1] 3
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             282 
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             282 
[1] "NAP1L2 MUTATION ANALYSIS"
[1] 3
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
              25              265 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
              25              265 
[1] "MPP7 MUTATION ANALYSIS"
[1] 3
  MPP7 MUTATED MPP7 WILD-TYPE 
            32            258 
  MPP7 MUTATED MPP7 WILD-TYPE 
            32            258 
[1] "BTK MUTATION ANALYSIS"
[1] 3
  BTK MUTATED BTK WILD-TYPE 
           15           275 
  BTK MUTATED BTK WILD-TYPE 
           15           275 
[1] "SLC9A11 MUTATION ANALYSIS"
[1] 3
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               44               246 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               44               246 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             7            283 
  EMG1 MUTATED EMG1 WILD-TYPE 
             7            283 
[1] "SELP MUTATION ANALYSIS"
[1] 3
  SELP MUTATED SELP WILD-TYPE 
            33            257 
  SELP MUTATED SELP WILD-TYPE 
            33            257 
[1] "PARM1 MUTATION ANALYSIS"
[1] 3
  PARM1 MUTATED PARM1 WILD-TYPE 
             19             271 
  PARM1 MUTATED PARM1 WILD-TYPE 
             19             271 
[1] "ACSBG1 MUTATION ANALYSIS"
[1] 3
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              13              277 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              13              277 
[1] "CCK MUTATION ANALYSIS"
[1] 3
  CCK MUTATED CCK WILD-TYPE 
            6           284 
  CCK MUTATED CCK WILD-TYPE 
            6           284 
[1] "C1QTNF9 MUTATION ANALYSIS"
[1] 3
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               274 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               274 
[1] "UBE2V2 MUTATION ANALYSIS"
[1] 3
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
               3              287 
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
               3              287 
[1] "BOLA1 MUTATION ANALYSIS"
[1] 3
  BOLA1 MUTATED BOLA1 WILD-TYPE 
              3             287 
  BOLA1 MUTATED BOLA1 WILD-TYPE 
              3             287 
[1] "IFNGR2 MUTATION ANALYSIS"
[1] 3
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              286 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              286 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             6            284 
  KRAS MUTATED KRAS WILD-TYPE 
             6            284 
[1] "ZNF595 MUTATION ANALYSIS"
[1] 3
  ZNF595 MUTATED ZNF595 WILD-TYPE 
               8              282 
  ZNF595 MUTATED ZNF595 WILD-TYPE 
               8              282 
[1] "PRKAA2 MUTATION ANALYSIS"
[1] 3
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              25              265 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              25              265 
[1] "MMP27 MUTATION ANALYSIS"
[1] 3
  MMP27 MUTATED MMP27 WILD-TYPE 
             13             277 
  MMP27 MUTATED MMP27 WILD-TYPE 
             13             277 
[1] "POLR2B MUTATION ANALYSIS"
[1] 3
  POLR2B MUTATED POLR2B WILD-TYPE 
              10              280 
  POLR2B MUTATED POLR2B WILD-TYPE 
              10              280 
[1] "CSN3 MUTATION ANALYSIS"
[1] 3
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            286 
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            286 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             281 
  CASP8 MUTATED CASP8 WILD-TYPE 
              9             281 
[1] "PPFIA1 MUTATION ANALYSIS"
[1] 3
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
              16              274 
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
              16              274 
[1] "ZNF490 MUTATION ANALYSIS"
[1] 3
  ZNF490 MUTATED ZNF490 WILD-TYPE 
              16              274 
  ZNF490 MUTATED ZNF490 WILD-TYPE 
              16              274 
[1] "IL5RA MUTATION ANALYSIS"
[1] 3
  IL5RA MUTATED IL5RA WILD-TYPE 
             16             274 
  IL5RA MUTATED IL5RA WILD-TYPE 
             16             274 
[1] "LILRB5 MUTATION ANALYSIS"
[1] 3
  LILRB5 MUTATED LILRB5 WILD-TYPE 
              19              271 
  LILRB5 MUTATED LILRB5 WILD-TYPE 
              19              271 
[1] "C10ORF72 MUTATION ANALYSIS"
[1] 3
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
                20                270 
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
                20                270 
[1] "C3ORF71 MUTATION ANALYSIS"
[1] 3
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               286 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               286 
[1] "ZNF589 MUTATION ANALYSIS"
[1] 3
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               3              287 
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               3              287 
[1] "DSP MUTATION ANALYSIS"
[1] 3
  DSP MUTATED DSP WILD-TYPE 
           60           230 
  DSP MUTATED DSP WILD-TYPE 
           60           230 
[1] "ZZZ3 MUTATION ANALYSIS"
[1] 3
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
             3            287 
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
             3            287 
[1] "MCART2 MUTATION ANALYSIS"
[1] 3
  MCART2 MUTATED MCART2 WILD-TYPE 
              10              280 
  MCART2 MUTATED MCART2 WILD-TYPE 
              10              280 
[1] "CD2 MUTATION ANALYSIS"
[1] 3
  CD2 MUTATED CD2 WILD-TYPE 
           22           268 
  CD2 MUTATED CD2 WILD-TYPE 
           22           268 
[1] "CD209 MUTATION ANALYSIS"
[1] 3
  CD209 MUTATED CD209 WILD-TYPE 
             12             278 
  CD209 MUTATED CD209 WILD-TYPE 
             12             278 
[1] "C2ORF16 MUTATION ANALYSIS"
[1] 3
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
               29               261 
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
               29               261 
[1] "GLRB MUTATION ANALYSIS"
[1] 3
  GLRB MUTATED GLRB WILD-TYPE 
            30            260 
  GLRB MUTATED GLRB WILD-TYPE 
            30            260 
[1] "PKDREJ MUTATION ANALYSIS"
[1] 3
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              30              260 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              30              260 
[1] "PTPRT MUTATION ANALYSIS"
[1] 3
  PTPRT MUTATED PTPRT WILD-TYPE 
             86             204 
  PTPRT MUTATED PTPRT WILD-TYPE 
             86             204 
[1] "FAM55C MUTATION ANALYSIS"
[1] 3
  FAM55C MUTATED FAM55C WILD-TYPE 
               6              284 
  FAM55C MUTATED FAM55C WILD-TYPE 
               6              284 
[1] "NUDT4 MUTATION ANALYSIS"
[1] 3
  NUDT4 MUTATED NUDT4 WILD-TYPE 
              5             285 
  NUDT4 MUTATED NUDT4 WILD-TYPE 
              5             285 
[1] "MYPOP MUTATION ANALYSIS"
[1] 3
  MYPOP MUTATED MYPOP WILD-TYPE 
              7             283 
  MYPOP MUTATED MYPOP WILD-TYPE 
              7             283 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            32            258 
  MLL4 MUTATED MLL4 WILD-TYPE 
            32            258 
[1] "MMP1 MUTATION ANALYSIS"
[1] 3
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            276 
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            276 
[1] "THEMIS MUTATION ANALYSIS"
[1] 3
  THEMIS MUTATED THEMIS WILD-TYPE 
              34              256 
  THEMIS MUTATED THEMIS WILD-TYPE 
              34              256 
[1] "ACO1 MUTATION ANALYSIS"
[1] 3
  ACO1 MUTATED ACO1 WILD-TYPE 
             8            282 
  ACO1 MUTATED ACO1 WILD-TYPE 
             8            282 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
            17            273 
  MUC7 MUTATED MUC7 WILD-TYPE 
            17            273 
[1] "TP63 MUTATION ANALYSIS"
[1] 3
  TP63 MUTATED TP63 WILD-TYPE 
            50            240 
  TP63 MUTATED TP63 WILD-TYPE 
            50            240 
[1] "APCS MUTATION ANALYSIS"
[1] 3
  APCS MUTATED APCS WILD-TYPE 
            13            277 
  APCS MUTATED APCS WILD-TYPE 
            13            277 
[1] "GPX5 MUTATION ANALYSIS"
[1] 3
  GPX5 MUTATED GPX5 WILD-TYPE 
            18            272 
  GPX5 MUTATED GPX5 WILD-TYPE 
            18            272 
[1] "PDK4 MUTATION ANALYSIS"
[1] 3
  PDK4 MUTATED PDK4 WILD-TYPE 
             7            283 
  PDK4 MUTATED PDK4 WILD-TYPE 
             7            283 
[1] "EPS8 MUTATION ANALYSIS"
[1] 3
  EPS8 MUTATED EPS8 WILD-TYPE 
             7            283 
  EPS8 MUTATED EPS8 WILD-TYPE 
             7            283 
[1] "LUZP1 MUTATION ANALYSIS"
[1] 3
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              6             284 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              6             284 
[1] "C10ORF118 MUTATION ANALYSIS"
[1] 3
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
                  7                 283 
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
                  7                 283 
[1] "OR51S1 MUTATION ANALYSIS"
[1] 3
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              30              260 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              30              260 
[1] "AMPD3 MUTATION ANALYSIS"
[1] 3
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             22             268 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             22             268 
[1] "CD300E MUTATION ANALYSIS"
[1] 3
  CD300E MUTATED CD300E WILD-TYPE 
              10              280 
  CD300E MUTATED CD300E WILD-TYPE 
              10              280 
[1] "SAG MUTATION ANALYSIS"
[1] 3
  SAG MUTATED SAG WILD-TYPE 
           11           279 
  SAG MUTATED SAG WILD-TYPE 
           11           279 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             282 
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             282 
[1] "RUFY4 MUTATION ANALYSIS"
[1] 3
  RUFY4 MUTATED RUFY4 WILD-TYPE 
             11             279 
  RUFY4 MUTATED RUFY4 WILD-TYPE 
             11             279 
[1] "MAP3K5 MUTATION ANALYSIS"
[1] 3
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              20              270 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              20              270 
[1] "NTN4 MUTATION ANALYSIS"
[1] 3
  NTN4 MUTATED NTN4 WILD-TYPE 
            15            275 
  NTN4 MUTATED NTN4 WILD-TYPE 
            15            275 
[1] "BCMO1 MUTATION ANALYSIS"
[1] 3
  BCMO1 MUTATED BCMO1 WILD-TYPE 
             17             273 
  BCMO1 MUTATED BCMO1 WILD-TYPE 
             17             273 
[1] "OR11H12 MUTATION ANALYSIS"
[1] 3
  OR11H12 MUTATED OR11H12 WILD-TYPE 
               15               275 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
               15               275 
[1] "SI MUTATION ANALYSIS"
[1] 3
  SI MUTATED SI WILD-TYPE 
          67          223 
  SI MUTATED SI WILD-TYPE 
          67          223 
[1] "ADAM33 MUTATION ANALYSIS"
[1] 3
  ADAM33 MUTATED ADAM33 WILD-TYPE 
              16              274 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
              16              274 
[1] "RICTOR MUTATION ANALYSIS"
[1] 3
  RICTOR MUTATED RICTOR WILD-TYPE 
              12              278 
  RICTOR MUTATED RICTOR WILD-TYPE 
              12              278 
[1] "MED17 MUTATION ANALYSIS"
[1] 3
  MED17 MUTATED MED17 WILD-TYPE 
              5             285 
  MED17 MUTATED MED17 WILD-TYPE 
              5             285 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "DAYS_TO_SUBMITTED_SPECIMEN_DX"       
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "MELANOMA_ULCERATION"                 
[11] "MELANOMA_PRIMARY_KNOWN"              
[12] "BRESLOW_THICKNESS"                   
[13] "GENDER"                              
[14] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[15] "RADIATION_THERAPY"                   
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 290 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=158,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=122,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DAYS_TO_SUBMITTED_SPECIMEN_DX':	nDistinctValues=231,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BRESLOW_THICKNESS':	nDistinctValues=99,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 290 columns, 2 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"         "PATHOLOGIC_STAGE"       "PATHOLOGY_T_STAGE"     
 [4] "PATHOLOGY_N_STAGE"      "PATHOLOGY_M_STAGE"      "MELANOMA_ULCERATION"   
 [7] "MELANOMA_PRIMARY_KNOWN" "BRESLOW_THICKNESS"      "GENDER"                
[10] "RADIATION_THERAPY"      "RACE"                   "ETHNICITY"             
YEARS_TO_BIRTH, nv=66, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
23 30 62 60 55 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53    62    60    55 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 30 62 60 55 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53    62    60    55 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
143  53  34  35 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
143  53  34  35 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
143  53  34  35 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
143  53  34  35 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
MELANOMA_ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA_PRIMARY_KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW_THICKNESS, nv=99, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, 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   24 35
  NRAS WILD-TYPE 73 68
  NRAS MUTATED NRAS WILD-TYPE 
            59            141 
  NRAS MUTATED NRAS WILD-TYPE 
            35             68 
$`NRAS MUTATED`
TCGA-EB-A5SG TCGA-EE-A2GD TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 
       33.24       269.03         8.42        19.04        62.60        62.86 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A51E TCGA-D3-A51R TCGA-D9-A3Z1 TCGA-DA-A1HV 
      171.58        66.08       173.85        62.70        15.02        76.34 
TCGA-DA-A1I1 TCGA-EB-A44Q TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q 
       68.68         3.91        13.15        75.55        44.28        61.12 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      115.43        30.02        68.65        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MM 
        0.76        81.99        23.77       209.79       104.78       145.45 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A195 
       53.26        64.04        45.90         3.35       135.98        34.45 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE 
        7.82        11.47        42.51       146.63        22.36        16.87 
TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZQ 
        4.50       171.78       195.98         8.35        43.92       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F9 TCGA-FS-A4FD 
       35.28        23.21         5.29         3.06        13.28        80.68 
TCGA-GF-A3OT TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
        9.90        17.06        42.48       120.53        34.49 

$`NRAS WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
       62.07        38.76        31.96       166.75        52.90       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       27.35        19.04        36.85        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
       49.35       133.25        76.41        25.64        45.99        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP 
      168.00        86.30       107.61        36.30        64.83        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T 
       90.21        23.67        30.67       144.46        31.76        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       42.05        45.70       177.86        22.29        69.21        22.85 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       30.44       225.11        42.64        16.41        52.41        18.21 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B 
       24.89        20.38         0.00        26.24        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14        12.99         0.26        47.41        47.74        27.16 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      346.49       185.19        77.98        26.14        12.95       201.60 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       10.62         0.20        71.31       103.13        15.25         5.75 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
       94.19       171.85        63.25        89.26       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       23.51       124.31       122.73         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19A 
       67.89       111.85       168.85        19.86        10.49         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81       184.60       150.12        99.06        59.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF 
      120.76        49.71        47.18        73.05         4.70        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A44A TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
      174.21        49.74        27.62       312.07        32.78         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-FS-A4F4 
       36.33        78.61       136.27         4.47        18.51        66.67 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
      173.19        55.59        11.54        19.30        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-OD-A75X 
       53.29       117.93        96.92         7.59        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  NRAS MUTATED NRAS WILD-TYPE 
          0.76           0.00 
  NRAS MUTATED NRAS WILD-TYPE 
        269.03         346.49 
  NRAS MUTATED NRAS WILD-TYPE 
         43.92          49.35 
[1] "0.8 - 269.0 (43.9)" "0.0 - 346.5 (49.4)"
[1] "hr=" "1.4"
D1V2, survival
                sevent
clus2              0   1
  NRAS MUTATED    32  53
  NRAS WILD-TYPE  92 107
  NRAS MUTATED NRAS WILD-TYPE 
            85            199 
  NRAS MUTATED NRAS WILD-TYPE 
            53            107 
$`NRAS MUTATED`
TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-D3-A1Q1 
       13.87        68.25        68.15         2.60       340.14        16.57 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3MV 
       28.08        95.74        65.49       171.58        66.08        45.30 
TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-DA-A1HV 
      174.84        63.81       137.92        15.39        25.18        76.57 
TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17X 
      222.51        10.49        13.87        10.36        29.29        29.82 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.96       151.27        72.07        66.74        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GJ 
       25.87        17.92       115.96        59.64        39.29       107.38 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2MC 
       79.66        75.48       102.12        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       216.66       167.90        47.54        53.26 
TCGA-EE-A3AC TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 
       64.04        64.08        34.32        53.19       152.81        35.44 
TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE 
        9.17        12.59        44.09       148.18        43.82        20.15 
TCGA-ER-A2NH TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       41.56        92.98        15.72       216.92       202.65        20.91 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       48.85        46.45        74.73       133.55        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.09        27.02        28.73        34.03        54.41        80.68 
TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
        9.90        15.78        64.44        62.79       121.91        39.35 
TCGA-GN-A4U9 
       22.13 

$`NRAS WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
       62.07        46.32        54.02        94.98       168.26       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 
      134.40        27.35        31.40        50.76        15.45        36.95 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       86.76        11.87       113.52        42.08        12.10        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F 
       60.23        24.53         9.34       103.59        39.75        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        22.62        26.89       125.79 
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-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        3.65         7.10        22.29         9.90        77.56        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89        20.38       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
      225.96        43.36        20.35        58.92         7.04        36.46 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
       27.22         8.65        33.73        14.70        26.89       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        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T 
       63.78        64.64        56.84        18.61        56.42       369.93 
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       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
      220.24        48.72        54.74        42.77        81.21        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       180.39       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      162.48        71.21       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
      201.80        51.35       134.33        13.94        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       302.07       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        49.48         8.88 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
      105.07        23.34        28.83        48.99       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1YX 
       46.98        33.21        12.95       149.03       174.21        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        28.08         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR 
        9.70        32.75        47.38        23.93       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
      148.80        26.56        77.82        66.67       174.84        26.73 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 
       17.46        55.59        13.51        19.30        19.43         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
      139.89       117.93        96.92        10.13        32.48        48.00 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       10.42        48.89       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  NRAS MUTATED NRAS WILD-TYPE 
           2.6            0.2 
  NRAS MUTATED NRAS WILD-TYPE 
        340.14         369.93 
  NRAS MUTATED NRAS WILD-TYPE 
         53.19          54.51 
[1] "2.6 - 340.1 (53.2)" "0.2 - 369.9 (54.5)"
[1] "hr=" "1.2"
D1V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  NRAS MUTATED          3       3       6        5       11        5         6
  NRAS WILD-TYPE        7       3      19        5       14       13         4
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NRAS MUTATED           5         2         6          4          7         17
  NRAS WILD-TYPE         9         8        30         10         19         26
                vv
clus             STAGE IV
  NRAS MUTATED          3
  NRAS WILD-TYPE       13
D1V4, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  I/II NOS              3              7
  STAGE 0               3              3
  STAGE I               6             19
  STAGE IA              5              5
  STAGE IB             11             14
  STAGE II              5             13
  STAGE IIA             6              4
  STAGE IIB             5              9
  STAGE IIC             2              8
  STAGE III             6             30
  STAGE IIIA            4             10
  STAGE IIIB            7             19
  STAGE IIIC           17             26
  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
  NRAS MUTATED      13 25 17 15
  NRAS WILD-TYPE    40 37 43 40
D1V5, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  T0+T1           13             40
  T2              25             37
  T3              17             43
  T4              15             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  NRAS MUTATED   47 10  9 15
  NRAS WILD-TYPE 96 43 25 20
D1V6, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0           47             96
  N1           10             43
  N2            9             25
  N3           15             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus               0   1
  NRAS MUTATED    79   3
  NRAS WILD-TYPE 177  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     79    3
  NRAS WILD-TYPE  177   14
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           79            177
  1            3             14
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus              0  1
  NRAS MUTATED   36 23
  NRAS WILD-TYPE 71 50
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     36   23
  NRAS WILD-TYPE   71   50
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            36             71
  YES           23             50
[1] 2 2
[1] FALSE
D1V9, binary
                cls
clus               0   1
  NRAS MUTATED    10  77
  NRAS WILD-TYPE  27 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     10   77
  NRAS WILD-TYPE   27  176
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            10             27
  YES           77            176
[1] 2 2
[1] FALSE
D1V10, continuous
D1V11, binary
                cls
clus               0   1
  NRAS MUTATED    30  57
  NRAS WILD-TYPE  79 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     30   57
  NRAS WILD-TYPE   79  124
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           30             79
  MALE             57            124
[1] 2 2
[1] FALSE
D1V12, binary
                cls
clus               0   1
  NRAS MUTATED    77  10
  NRAS WILD-TYPE 177  25
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     77   10
  NRAS WILD-TYPE  177   25
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            77            177
  YES           10             25
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       2                         0    85
  NRAS WILD-TYPE     3                         1   199
D1V13, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                2              3
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               85            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"
D1V14, binary
                cls
clus               0   1
  NRAS MUTATED     1  85
  NRAS WILD-TYPE   2 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1   85
  NRAS WILD-TYPE    2  198
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           85            198
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   21 13
  TP53 WILD-TYPE 76 90
  TP53 MUTATED TP53 WILD-TYPE 
            34            166 
  TP53 MUTATED TP53 WILD-TYPE 
            13             90 
$`TP53 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A51T 
       38.76        27.35        36.85        76.41        15.75        11.34 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-EE-A181 
       45.70       177.86        69.21        76.34       110.53        20.38 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2MG 
        0.26        47.74        30.02        68.65         0.76        94.19 
TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J7 
      145.45        53.26       124.31         4.41        54.51        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZW 
        3.35       135.98         7.82        68.52        27.62        23.21 
TCGA-FS-A4F9 TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-OD-A75X 
       13.28         1.91       120.53       297.01 

$`TP53 WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
      134.40        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        19.04        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A3Z1 
       30.67       144.46        31.76        62.70        42.05        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 
       22.29        22.85       138.67        68.68       150.61        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
      115.43        77.98        26.14        12.95       201.60        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35        93.63         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI 
      103.13        15.25         5.75        23.77       209.79       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       227.01       143.93        23.51 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB 
      122.73        64.04         6.28        67.89       111.85       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       19.86        34.45        10.49         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
        4.70        16.87        10.19        28.67       173.29        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98         8.35       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD 
        5.29         3.06        18.51        66.67       173.19        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
       55.59        11.54        19.30         9.90        18.25        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 
      117.93        96.92        17.06        42.48         7.59        34.49 
TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92         7.23         0.20         0.33 

  TP53 MUTATED TP53 WILD-TYPE 
          0.26           0.00 
  TP53 MUTATED TP53 WILD-TYPE 
        297.01         346.49 
  TP53 MUTATED TP53 WILD-TYPE 
         45.80          48.38 
[1] "0.3 - 297.0 (45.8)" "0.0 - 346.5 (48.4)"
[1] "hr=" "1.3"
D2V2, survival
                sevent
clus2              0   1
  TP53 MUTATED    26  21
  TP53 WILD-TYPE  98 139
  TP53 MUTATED TP53 WILD-TYPE 
            47            237 
  TP53 MUTATED TP53 WILD-TYPE 
            21            139 
$`TP53 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A29L TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A2JA 
       46.32         2.60        27.35        36.95        90.90       115.53 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A6EA TCGA-D9-A6EC 
       26.89       135.75       137.92       178.32        25.18        77.56 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29M 
       76.57        36.03       135.02        33.73        63.78        56.84 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT 
       17.92        59.64        67.43       107.38        13.91        44.88 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD 
      103.20       167.90        43.23        53.26       124.31        28.77 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI 
       54.51        41.59        36.95        64.08        34.32       152.81 
TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZW TCGA-FS-A4F9 
        9.17        13.02        93.01        28.08        49.48        34.03 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-OD-A75X 
        2.04        15.78        10.13       121.91       297.90 

$`TP53 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 
      168.26       340.14       126.81       134.40        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        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        66.48        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-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-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      125.79        18.18       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HY 
        7.10        15.39        22.29         9.90        22.95       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       222.51       176.55        35.93        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
        7.04        36.46        29.82        27.22         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        13.97        72.07        64.64 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
       25.87       195.02        46.82       115.96        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       173.79       220.24        48.72        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       75.48       102.12        42.77        81.21        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-A2ML 
      268.73        16.96       204.66        96.23       180.39       216.66 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       47.54       248.65       162.48        71.21       122.73        64.04 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JB 
       13.81       138.81       172.18       127.20        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       51.35       134.33        35.44        13.94        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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       28.83        48.99        41.56       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        92.98       174.21        15.72       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73       174.84        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       48.00        39.35        10.42        48.89        22.13         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  TP53 MUTATED TP53 WILD-TYPE 
          2.04           0.20 
  TP53 MUTATED TP53 WILD-TYPE 
        297.90         369.93 
  TP53 MUTATED TP53 WILD-TYPE 
         49.48          54.41 
[1] "2.0 - 297.9 (49.5)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.2"
D2V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  TP53 MUTATED          0       1       6        3        4        2         1
  TP53 WILD-TYPE       10       5      19        7       21       16         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TP53 MUTATED           2         0         8          5          6          7
  TP53 WILD-TYPE        12        10        28          9         20         36
                vv
clus             STAGE IV
  TP53 MUTATED          1
  TP53 WILD-TYPE       15
D2V4, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               1              5
  STAGE I               6             19
  STAGE IA              3              7
  STAGE IB              4             21
  STAGE II              2             16
  STAGE IIA             1              9
  STAGE IIB             2             12
  STAGE IIC             0             10
  STAGE III             8             28
  STAGE IIIA            5              9
  STAGE IIIB            6             20
  STAGE IIIC            7             36
  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    41 52 51 45
D2V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           12             41
  T2              10             52
  T3               9             51
  T4              10             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TP53 MUTATED    19  14   6   5
  TP53 WILD-TYPE 124  39  28  30
D2V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           19            124
  N1           14             39
  N2            6             28
  N3            5             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"
D2V7, binary
                cls
clus               0   1
  TP53 MUTATED    45   1
  TP53 WILD-TYPE 211  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     45    1
  TP53 WILD-TYPE  211   16
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           45            211
  1            1             16
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus              0  1
  TP53 MUTATED   20 10
  TP53 WILD-TYPE 87 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     20   10
  TP53 WILD-TYPE   87   63
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            20             87
  YES           10             63
[1] 2 2
[1] FALSE
D2V9, binary
                cls
clus               0   1
  TP53 MUTATED     7  41
  TP53 WILD-TYPE  30 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      7   41
  TP53 WILD-TYPE   30  212
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             7             30
  YES           41            212
[1] 2 2
[1] FALSE
D2V10, continuous
D2V11, binary
                cls
clus               0   1
  TP53 MUTATED    17  31
  TP53 WILD-TYPE  92 150
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     17   31
  TP53 WILD-TYPE   92  150
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           17             92
  MALE             31            150
[1] 2 2
[1] FALSE
D2V12, binary
                cls
clus               0   1
  TP53 MUTATED    40   8
  TP53 WILD-TYPE 214  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     40    8
  TP53 WILD-TYPE  214   27
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            40            214
  YES            8             27
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0    48
  TP53 WILD-TYPE     5                         1   236
D2V13, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               48            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"
D2V14, binary
                cls
clus               0   1
  TP53 MUTATED     0  48
  TP53 WILD-TYPE   3 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   48
  TP53 WILD-TYPE    3  235
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           48            235
[1] 2 2
[1] FALSE

Clustering(3) Variable = CDKN2A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED   17 10
  CDKN2A WILD-TYPE 80 93
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              27              173 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              10               93 
$`CDKN2A MUTATED`
TCGA-D3-A2JF TCGA-EE-A3JD TCGA-D3-A1Q4 TCGA-D3-A3CB TCGA-D3-A51J TCGA-D3-A5GN 
       62.07        27.35        31.89       140.98       144.46        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        15.02        69.21        22.85        76.34       138.67 
TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A3AE 
       20.38         0.26        77.98        18.35         0.76        54.51 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P 
       45.90       168.85        11.47       150.12        99.06       120.76 
TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-GF-A4EO 
      130.95        23.21        18.25 

$`CDKN2A WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
      134.40        19.04        36.85         8.42        15.72       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85        30.67        31.76        62.70        11.34        42.05 
TCGA-D9-A3Z3 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.29        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        24.89         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       75.55        79.20        75.22        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        30.02        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       10.62        32.48        93.63         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH 
        4.41         6.28        67.89       111.85         3.35        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
       39.81       184.60        59.84        42.51        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       78.61       136.27        35.28         4.47         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       11.54        19.30         9.90         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.26             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          177.86           346.49 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           54.51            47.18 
[1] "0.3 - 177.9 (54.5)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.5"
D3V2, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    22  17
  CDKN2A WILD-TYPE 102 143
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              39              245 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              17              143 
$`CDKN2A MUTATED`
TCGA-D3-A2JF TCGA-EE-A3JD TCGA-D3-A1Q4 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CB 
       62.07        27.35       112.04        11.87        12.10       166.52 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 
       45.30       145.12       135.75       178.32        18.18        15.39 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A185 
       77.56        22.95        76.57       144.89        33.73         4.96 
TCGA-EE-A20B TCGA-EE-A29E TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GM 
      133.81        63.78        25.87        86.14        67.43        75.48 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J7 
       13.91        21.67        47.28        54.51        41.59        64.08 
TCGA-EE-A3JB TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-FS-A1ZQ 
      201.80        12.59       152.35       131.51       162.08       133.55 
TCGA-FS-A1ZW TCGA-GF-A4EO TCGA-RP-A694 
       49.48        19.43         0.69 

$`CDKN2A WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
      168.26         2.60       340.14       126.81       134.40        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       50.76        15.45        36.95        16.57        16.67       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.76       113.52        42.08       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57       130.72        58.06        46.98        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34       103.59        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      137.92       125.19       151.53        54.67         3.65         7.10 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.29         9.90        25.18        36.03        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       36.46        29.82        27.22         8.65        14.70        26.89 
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        85.08        78.97 
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-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       66.74        14.47        61.28       369.93       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GE 
       46.82       115.96        59.64        39.29        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      220.24        48.72       107.38        54.74        79.66       102.12 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82       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       180.39       216.66       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-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        64.04        28.77        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        36.95        34.32        53.19        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       48.89        13.02        26.37       302.07         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.09        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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-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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       55.59        13.51        19.30         9.90         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       22.13       297.90         7.23         0.20         0.33 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.69             0.20 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          201.80           369.93 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           62.07            53.52 
[1] "0.7 - 201.8 (62.1)" "0.2 - 369.9 (53.5)"
[1] "hr=" "1.2"
D3V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CDKN2A MUTATED          3       0       3        3        1        3
  CDKN2A WILD-TYPE        7       6      22        7       24       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CDKN2A MUTATED           0         1         1         6          2
  CDKN2A WILD-TYPE        10        13         9        30         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CDKN2A MUTATED            5          7        3
  CDKN2A WILD-TYPE         21         36       13
D3V4, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  I/II NOS                3                7
  STAGE 0                 0                6
  STAGE I                 3               22
  STAGE IA                3                7
  STAGE IB                1               24
  STAGE II                3               15
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               1                9
  STAGE III               6               30
  STAGE IIIA              2               12
  STAGE IIIB              5               21
  STAGE IIIC              7               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
  CDKN2A MUTATED      10 10  8  6
  CDKN2A WILD-TYPE    43 52 52 49
D3V5, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1             10               43
  T2                10               52
  T3                 8               52
  T4                 6               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN2A MUTATED    17  13   5   3
  CDKN2A WILD-TYPE 126  40  29  32
D3V6, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             17              126
  N1             13               40
  N2              5               29
  N3              3               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"
D3V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    37   3
  CDKN2A WILD-TYPE 219  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     37    3
  CDKN2A WILD-TYPE  219   14
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             37              219
  1              3               14
[1] 2 2
[1] FALSE
D3V8, binary
                  cls
clus                0  1
  CDKN2A MUTATED    8 14
  CDKN2A WILD-TYPE 99 59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      8   14
  CDKN2A WILD-TYPE   99   59
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               8               99
  YES             14               59
[1] 2 2
[1] FALSE
D3V9, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     6  35
  CDKN2A WILD-TYPE  31 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      6   35
  CDKN2A WILD-TYPE   31  218
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               6               31
  YES             35              218
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    15  26
  CDKN2A WILD-TYPE  94 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     15   26
  CDKN2A WILD-TYPE   94  155
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             15               94
  MALE               26              155
[1] 2 2
[1] FALSE
D3V12, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    38   3
  CDKN2A WILD-TYPE 216  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     38    3
  CDKN2A WILD-TYPE  216   32
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              38              216
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       0                         0    41
  CDKN2A WILD-TYPE     5                         1   243
D3V13, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 41              243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     0  41
  CDKN2A WILD-TYPE   3 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   41
  CDKN2A WILD-TYPE    3  242
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             41              242
[1] 2 2
[1] FALSE

Clustering(4) Variable = NF1 MUTATION ANALYSIS
D4V1, survival
               sevent
clus2            0  1
  NF1 MUTATED   12 14
  NF1 WILD-TYPE 85 89
  NF1 MUTATED NF1 WILD-TYPE 
           26           174 
  NF1 MUTATED NF1 WILD-TYPE 
           14            89 
$`NF1 MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JA 
       62.07        31.96        52.90        27.35        36.85        15.75 
TCGA-D3-A51R TCGA-D9-A6EC TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       62.70        69.21        58.85        13.15        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS 
       75.55        30.02         0.20       171.85        63.25       143.93 
TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19A TCGA-FS-A1Z3 TCGA-FS-A1ZZ TCGA-FS-A4F4 
       23.51        54.51         4.54         8.35         3.06        66.67 
TCGA-FW-A3TU TCGA-GF-A4EO 
       55.59        18.25 

$`NF1 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 
       38.76        33.24       166.75       269.03       134.40        19.04 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        31.76        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        22.29        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61       110.53        60.10        64.83        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
       42.64         3.91        16.41        52.41        18.21        24.89 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       26.24        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19       115.43        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      209.79        94.19        89.26       104.78       145.45       227.01 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        64.04         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      135.98        34.45        10.49         7.82        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74       195.98        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
        4.47        23.21         5.29        18.51       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       80.68        11.54        19.30         9.90         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  NF1 MUTATED NF1 WILD-TYPE 
          0.0           0.2 
  NF1 MUTATED NF1 WILD-TYPE 
       171.85        346.49 
  NF1 MUTATED NF1 WILD-TYPE 
       34.405        47.575 
[1] "0.0 - 171.8 (34.4)" "0.2 - 346.5 (47.6)"
[1] "hr=" "1.7"
D4V2, survival
               sevent
clus2             0   1
  NF1 MUTATED    15  23
  NF1 WILD-TYPE 109 137
  NF1 MUTATED NF1 WILD-TYPE 
           38           246 
  NF1 MUTATED NF1 WILD-TYPE 
           23           137 
$`NF1 MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 
       62.07        94.98         2.60       126.81        27.35        36.95 
TCGA-D3-A2JA TCGA-D3-A51R TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X 
      115.53        63.81        77.56        20.38        68.09        29.82 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 
       33.73        14.70       151.27        18.61        25.87        59.64 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS 
       67.43        48.72        42.77       204.66        96.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-ER-A19A TCGA-ER-A19F TCGA-FS-A1Z3 
       71.21        54.51        36.95        77.75        26.37        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FW-A3I3 TCGA-FW-A3TU 
       27.72        74.73        27.02        66.67        17.46        55.59 
TCGA-GF-A4EO TCGA-GN-A266 
       19.43        10.13 

$`NF1 WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H 
       46.32        13.87        68.25        54.02        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 
      340.14       134.40        31.40        50.76        15.45        16.57 
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-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-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        22.62        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       25.18        22.95        76.57        36.03       144.89       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       40.60        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       27.22         8.65        26.89         4.96       133.81        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        56.84        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       61.28       369.93       195.02        17.92        46.82       115.96 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       39.29        86.14        59.28       173.79       220.24       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       54.74        79.66        75.48       102.12        13.91        81.21 
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 
      180.39       216.66       167.90        47.54       248.65        43.23 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        64.04        28.77        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       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       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       13.94         9.17        98.40        48.89        12.59        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        28.08         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.09        77.82        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       54.41        80.68        13.51        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.78       139.89       117.93        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  NF1 MUTATED NF1 WILD-TYPE 
          2.6           0.2 
  NF1 MUTATED NF1 WILD-TYPE 
       204.66        369.93 
  NF1 MUTATED NF1 WILD-TYPE 
       51.615        53.970 
[1] "2.6 - 204.7 (51.6)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.4"
D4V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  NF1 MUTATED          1       1       0        4        1        6         1
  NF1 WILD-TYPE        9       5      25        6       24       12         9
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NF1 MUTATED           3         0         5          2          2          5
  NF1 WILD-TYPE        11        10        31         12         24         38
               vv
clus            STAGE IV
  NF1 MUTATED          4
  NF1 WILD-TYPE       12
D4V4, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  I/II NOS             1             9
  STAGE 0              1             5
  STAGE I              0            25
  STAGE IA             4             6
  STAGE IB             1            24
  STAGE II             6            12
  STAGE IIA            1             9
  STAGE IIB            3            11
  STAGE IIC            0            10
  STAGE III            5            31
  STAGE IIIA           2            12
  STAGE IIIB           2            24
  STAGE IIIC           5            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
  NF1 MUTATED       5  2 11 10
  NF1 WILD-TYPE    48 60 49 45
D4V5, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  T0+T1           5            48
  T2              2            60
  T3             11            49
  T4             10            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NF1 MUTATED    23   6   4   3
  NF1 WILD-TYPE 120  47  30  32
D4V6, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0          23           120
  N1           6            47
  N2           4            30
  N3           3            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"
D4V7, binary
               cls
clus              0   1
  NF1 MUTATED    32   4
  NF1 WILD-TYPE 224  13
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     32    4
  NF1 WILD-TYPE  224   13
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          32           224
  1           4            13
[1] 2 2
[1] FALSE
D4V8, binary
               cls
clus             0  1
  NF1 MUTATED   14  9
  NF1 WILD-TYPE 93 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     14    9
  NF1 WILD-TYPE   93   64
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           14            93
  YES           9            64
[1] 2 2
[1] FALSE
D4V9, binary
               cls
clus              0   1
  NF1 MUTATED     6  32
  NF1 WILD-TYPE  31 221
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6   32
  NF1 WILD-TYPE   31  221
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            6            31
  YES          32           221
[1] 2 2
[1] FALSE
D4V10, continuous
D4V11, binary
               cls
clus              0   1
  NF1 MUTATED    10  28
  NF1 WILD-TYPE  99 153
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     10   28
  NF1 WILD-TYPE   99  153
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          10            99
  MALE            28           153
[1] 2 2
[1] FALSE
D4V12, binary
               cls
clus              0   1
  NF1 MUTATED    34   4
  NF1 WILD-TYPE 220  31
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     34    4
  NF1 WILD-TYPE  220   31
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           34           220
  YES           4            31
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED       0                         0    38
  NF1 WILD-TYPE     5                         1   246
D4V13, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              38           246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
               cls
clus              0   1
  NF1 MUTATED     1  35
  NF1 WILD-TYPE   2 248
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   35
  NF1 WILD-TYPE    2  248
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          35           248
[1] 2 2
[1] FALSE

Clustering(5) Variable = PTEN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    9  7
  PTEN WILD-TYPE 88 96
  PTEN MUTATED PTEN WILD-TYPE 
            16            184 
  PTEN MUTATED PTEN WILD-TYPE 
             7             96 
$`PTEN MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A51T 
       31.89       133.25        62.86        58.06        90.21        11.34 
TCGA-D3-A5GN TCGA-D9-A6EC TCGA-EE-A29P TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU 
       45.70        69.21        27.16        93.63        71.31        81.99 
TCGA-ER-A2NE TCGA-FS-A1ZD TCGA-GN-A4U8 TCGA-OD-A75X 
       16.87        32.78        46.92       297.01 

$`PTEN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       15.72       110.93        49.35        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       25.64        45.99        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB 
       36.30       171.58        64.83        66.08        43.53       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        59.70        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR 
       30.67       144.46        31.76        62.70        42.05       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        22.29        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M6 
       10.62        32.48        18.35         0.76         0.20       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05        22.36         4.70        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49         7.23         0.20         0.33 

  PTEN MUTATED PTEN WILD-TYPE 
         11.34           0.00 
  PTEN MUTATED PTEN WILD-TYPE 
        297.01         346.49 
  PTEN MUTATED PTEN WILD-TYPE 
        60.460         46.585 
[1] "11.3 - 297.0 (60.5)" "0.0 - 346.5 (46.6)" 
[1] "hr=" "1.3"
D5V2, survival
                sevent
clus2              0   1
  PTEN MUTATED    12  13
  PTEN WILD-TYPE 112 147
  PTEN MUTATED PTEN WILD-TYPE 
            25            259 
  PTEN MUTATED PTEN WILD-TYPE 
            13            147 
$`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        77.56         8.65        56.42       102.12 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A3AH TCGA-EE-A3JE TCGA-ER-A19E TCGA-ER-A19J 
       81.21        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 TCGA-GN-A4U8 
       20.15        12.95        15.72        53.52        17.46        48.89 
TCGA-OD-A75X 
      297.90 

$`PTEN WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67       112.57        71.80        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74        43.43       103.10        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       86.76        11.87       113.52        42.08       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        59.57       130.72        46.98       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-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      125.79       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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
        7.04        36.46        29.82        27.22        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64        56.84        18.61        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        42.77        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19       201.80       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
        9.17        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      302.07       152.35       131.51        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       46.98        33.21       149.03        92.98       174.21       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85       357.37        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       39.35        10.42        22.13         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  PTEN MUTATED PTEN WILD-TYPE 
          6.44           0.20 
  PTEN MUTATED PTEN WILD-TYPE 
        297.90         369.93 
  PTEN MUTATED PTEN WILD-TYPE 
         56.42          53.92 
[1] "6.4 - 297.9 (56.4)" "0.2 - 369.9 (53.9)"
[1] "hr=" "1"  
D5V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PTEN MUTATED          0       1       1        1        5        1         2
  PTEN WILD-TYPE       10       5      24        9       20       17         8
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PTEN MUTATED           1         1         1          1          1          5
  PTEN WILD-TYPE        13         9        35         13         25         38
                vv
clus             STAGE IV
  PTEN MUTATED          2
  PTEN WILD-TYPE       14
D5V4, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  I/II NOS              0             10
  STAGE 0               1              5
  STAGE I               1             24
  STAGE IA              1              9
  STAGE IB              5             20
  STAGE II              1             17
  STAGE IIA             2              8
  STAGE IIB             1             13
  STAGE IIC             1              9
  STAGE III             1             35
  STAGE IIIA            1             13
  STAGE IIIB            1             25
  STAGE IIIC            5             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
  PTEN MUTATED       4  7  3  5
  PTEN WILD-TYPE    49 55 57 50
D5V5, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            4             49
  T2               7             55
  T3               3             57
  T4               5             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PTEN MUTATED    14   5   1   3
  PTEN WILD-TYPE 129  48  33  32
D5V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           14            129
  N1            5             48
  N2            1             33
  N3            3             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"
D5V7, binary
                cls
clus               0   1
  PTEN MUTATED    21   2
  PTEN WILD-TYPE 235  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     21    2
  PTEN WILD-TYPE  235   15
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           21            235
  1            2             15
[1] 2 2
[1] FALSE
D5V8, binary
                cls
clus              0  1
  PTEN MUTATED    9  8
  PTEN WILD-TYPE 98 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      9    8
  PTEN WILD-TYPE   98   65
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             9             98
  YES            8             65
[1] 2 2
[1] FALSE
D5V9, binary
                cls
clus               0   1
  PTEN MUTATED     4  21
  PTEN WILD-TYPE  33 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4   21
  PTEN WILD-TYPE   33  232
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             4             33
  YES           21            232
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, binary
                cls
clus               0   1
  PTEN MUTATED    12  13
  PTEN WILD-TYPE  97 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     12   13
  PTEN WILD-TYPE   97  168
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           12             97
  MALE             13            168
[1] 2 2
[1] FALSE
D5V12, binary
                cls
clus               0   1
  PTEN MUTATED    19   6
  PTEN WILD-TYPE 235  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     19    6
  PTEN WILD-TYPE  235   29
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            19            235
  YES            6             29
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0    25
  PTEN WILD-TYPE     5                         1   259
D5V13, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               25            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"
D5V14, binary
                cls
clus               0   1
  PTEN MUTATED     0  25
  PTEN WILD-TYPE   3 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   25
  PTEN WILD-TYPE    3  258
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           25            258
[1] 2 2
[1] FALSE

Clustering(6) Variable = RAC1 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  RAC1 MUTATED    9  6
  RAC1 WILD-TYPE 88 97
  RAC1 MUTATED RAC1 WILD-TYPE 
            15            185 
  RAC1 MUTATED RAC1 WILD-TYPE 
             6             97 
$`RAC1 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-D3-A2JH TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R 
       38.76        27.35        36.30        90.21        23.67        62.70 
TCGA-D9-A3Z1 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2GM TCGA-EE-A3AB TCGA-ER-A199 
       15.02        20.38        12.99        18.35       122.73         7.82 
TCGA-ER-A1A1 TCGA-FS-A1ZU TCGA-QB-A6FS 
       73.05         4.47         7.23 

$`RAC1 WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
      134.40        19.04        36.85         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
      107.61       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E 
      140.98        40.01        59.70        24.53         9.34       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       144.46        31.76        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        24.89         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
      227.01       143.93        23.51        53.26       124.31        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      130.95       136.27        35.28        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         0.20         0.33 

  RAC1 MUTATED RAC1 WILD-TYPE 
          4.47           0.00 
  RAC1 MUTATED RAC1 WILD-TYPE 
        122.73         346.49 
  RAC1 MUTATED RAC1 WILD-TYPE 
         23.67          49.71 
[1] "4.5 - 122.7 (23.7)" "0.0 - 346.5 (49.7)"
[1] "hr=" "1.4"
D6V2, survival
                sevent
clus2              0   1
  RAC1 MUTATED     9  11
  RAC1 WILD-TYPE 115 149
  RAC1 MUTATED RAC1 WILD-TYPE 
            20            264 
  RAC1 MUTATED RAC1 WILD-TYPE 
            11            149 
$`RAC1 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-D3-A2JH TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R 
       46.32        27.35        42.08       103.59        39.75        63.81 
TCGA-D9-A3Z1 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A3AB 
       15.39        33.73        13.97        75.48        21.67       122.73 
TCGA-ER-A199 TCGA-ER-A1A1 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
        9.17       105.07        27.72        23.93        74.73        26.56 
TCGA-GN-A266 TCGA-QB-A6FS 
       10.13         7.23 

$`RAC1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
      168.26         2.60       340.14       126.81       134.40        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JK TCGA-D3-A2JL 
      168.00        86.76        11.87       113.52        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       66.48        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
      166.52        86.93        60.23        24.53         9.34        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-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        8.65        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56        13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66       102.12        13.91        42.77        81.21        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 
      180.39       216.66       167.90        47.54       248.65        43.23 
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        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       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-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
      134.33       152.81        35.44        13.94        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       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.48         8.88       148.18        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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-A1ZG 
        7.79        48.85       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2.04        15.78       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13       297.90         0.20         0.33         0.69 

  RAC1 MUTATED RAC1 WILD-TYPE 
          7.23           0.20 
  RAC1 MUTATED RAC1 WILD-TYPE 
        122.73         369.93 
  RAC1 MUTATED RAC1 WILD-TYPE 
        30.725         54.705 
[1] "7.2 - 122.7 (30.7)" "0.2 - 369.9 (54.7)"
[1] "hr=" "1.7"
D6V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  RAC1 MUTATED          0       0       1        0        1        3         1
  RAC1 WILD-TYPE       10       6      24       10       24       15         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RAC1 MUTATED           0         2         3          1          1          6
  RAC1 WILD-TYPE        14         8        33         13         25         37
                vv
clus             STAGE IV
  RAC1 MUTATED          0
  RAC1 WILD-TYPE       16
D6V4, multiclass
            clus
vv           RAC1 MUTATED RAC1 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               1             24
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              3             15
  STAGE IIA             1              9
  STAGE IIB             0             14
  STAGE IIC             2              8
  STAGE III             3             33
  STAGE IIIA            1             13
  STAGE IIIB            1             25
  STAGE IIIC            6             37
  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    49 60 55 50
D6V5, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  T0+T1            4             49
  T2               2             60
  T3               5             55
  T4               5             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RAC1 MUTATED     8   2   4   5
  RAC1 WILD-TYPE 135  51  30  30
D6V6, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  N0            8            135
  N1            2             51
  N2            4             30
  N3            5             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"
D6V7, binary
                cls
clus               0   1
  RAC1 MUTATED    19   0
  RAC1 WILD-TYPE 237  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED     19    0
  RAC1 WILD-TYPE  237   17
   clus
vv  RAC1 MUTATED RAC1 WILD-TYPE
  0           19            237
  1            0             17
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus               0   1
  RAC1 MUTATED     4   5
  RAC1 WILD-TYPE 103  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      4    5
  RAC1 WILD-TYPE  103   68
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             4            103
  YES            5             68
[1] 2 2
[1] FALSE
D6V9, binary
                cls
clus               0   1
  RAC1 MUTATED     6  14
  RAC1 WILD-TYPE  31 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      6   14
  RAC1 WILD-TYPE   31  239
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             6             31
  YES           14            239
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, binary
                cls
clus               0   1
  RAC1 MUTATED     6  14
  RAC1 WILD-TYPE 103 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      6   14
  RAC1 WILD-TYPE  103  167
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            6            103
  MALE             14            167
[1] 2 2
[1] FALSE
D6V12, binary
                cls
clus               0   1
  RAC1 MUTATED    15   5
  RAC1 WILD-TYPE 239  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED     15    5
  RAC1 WILD-TYPE  239   30
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO            15            239
  YES            5             30
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED       0                         0    20
  RAC1 WILD-TYPE     5                         1   264
D6V13, multiclass
                           clus
vv                          RAC1 MUTATED RAC1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               20            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"
D6V14, binary
                cls
clus               0   1
  RAC1 MUTATED     0  20
  RAC1 WILD-TYPE   3 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0   20
  RAC1 WILD-TYPE    3  263
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           20            263
[1] 2 2
[1] FALSE

Clustering(7) Variable = ARID2 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2              0  1
  ARID2 MUTATED   11 11
  ARID2 WILD-TYPE 86 92
  ARID2 MUTATED ARID2 WILD-TYPE 
             22             178 
  ARID2 MUTATED ARID2 WILD-TYPE 
             11              92 
$`ARID2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2JO TCGA-D3-A3MR 
       62.07       269.03        19.04        36.85        66.08        90.21 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D9-A6EC TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29P 
       42.05       177.86        69.21        58.85         0.00        27.16 
TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2MC TCGA-EE-A3AC TCGA-EE-A3AF TCGA-FS-A1Z3 
       30.02        68.65        23.77        64.04         6.28         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZZ TCGA-GN-A4U4 
      312.07        32.78         3.06        34.49 

$`ARID2 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
       38.76        33.24        31.96       166.75        52.90       134.40 
TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       27.35         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        64.83        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       59.70        24.53         9.34        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D9-A3Z1 
      144.46        31.76        62.70        11.34        45.70        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.29        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        60.10        64.83        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       12.99         0.26        44.28        47.41        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      346.49       185.19       115.43        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      201.60        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73         4.41        54.51        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       27.62        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      136.27        35.28         4.47        23.21         5.29        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 
       96.92        17.06        42.48         7.59       120.53        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  ARID2 MUTATED ARID2 WILD-TYPE 
            0.0             0.2 
  ARID2 MUTATED ARID2 WILD-TYPE 
         312.07          346.49 
  ARID2 MUTATED ARID2 WILD-TYPE 
         39.450          47.575 
[1] "0.0 - 312.1 (39.5)" "0.2 - 346.5 (47.6)"
[1] "hr=" "1.1"
D7V2, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    14  22
  ARID2 WILD-TYPE 110 138
  ARID2 MUTATED ARID2 WILD-TYPE 
             36             248 
  ARID2 MUTATED ARID2 WILD-TYPE 
             22             138 
$`ARID2 MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EE-A2GD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2JO 
       62.07        13.87       340.14        31.40        36.95        66.08 
TCGA-D3-A3MR TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A1I4 
      103.59       125.79       178.32       125.19        77.56        35.93 
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A2 
       68.09        14.70        18.61        56.42        61.28        59.64 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AF 
       48.72       107.38        61.51        47.28        64.04        13.81 
TCGA-EE-A3AG TCGA-EE-A3JE TCGA-ER-A19E TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       41.59        51.35        13.02        20.91       357.37        53.52 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-GN-A266 TCGA-GN-A4U4 
       74.73        27.02        28.73        54.41        10.13        39.35 

$`ARID2 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       46.32        68.25        54.02        94.98        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF 
        2.60       126.81       134.40        27.35        50.76        15.45 
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        66.48        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-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-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      135.75       137.92        18.18       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        7.10        15.39        22.29         9.90        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
      135.02        88.87        53.92        65.92        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        8.65        33.73        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
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        66.74        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
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       173.79       220.24 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        44.88        94.82        21.67       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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       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-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       28.77        54.51       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32        53.19       201.80       134.33       152.81 
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-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       48.85        46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       96.92        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ARID2 MUTATED ARID2 WILD-TYPE 
          10.13            0.20 
  ARID2 MUTATED ARID2 WILD-TYPE 
         357.37          369.93 
  ARID2 MUTATED ARID2 WILD-TYPE 
         53.965          53.970 
[1] "10.1 - 357.4 (54.0)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1.1"
D7V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ARID2 MUTATED          3       0       1        3        4        2         4
  ARID2 WILD-TYPE        7       6      24        7       21       16         6
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ARID2 MUTATED           3         1         5          2          2
  ARID2 WILD-TYPE        11         9        31         12         24
                 vv
clus              STAGE IIIC STAGE IV
  ARID2 MUTATED            5        1
  ARID2 WILD-TYPE         38       15
D7V4, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  I/II NOS               3               7
  STAGE 0                0               6
  STAGE I                1              24
  STAGE IA               3               7
  STAGE IB               4              21
  STAGE II               2              16
  STAGE IIA              4               6
  STAGE IIB              3              11
  STAGE IIC              1               9
  STAGE III              5              31
  STAGE IIIA             2              12
  STAGE IIIB             2              24
  STAGE IIIC             5              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
  ARID2 MUTATED       9  7 11  4
  ARID2 WILD-TYPE    44 55 49 51
D7V5, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  T0+T1             9              44
  T2                7              55
  T3               11              49
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ARID2 MUTATED    21   6   6   2
  ARID2 WILD-TYPE 122  47  28  33
D7V6, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            21             122
  N1             6              47
  N2             6              28
  N3             2              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"
D7V7, binary
                 cls
clus                0   1
  ARID2 MUTATED    35   1
  ARID2 WILD-TYPE 221  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     35    1
  ARID2 WILD-TYPE  221   16
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            35             221
  1             1              16
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus               0  1
  ARID2 MUTATED   14 11
  ARID2 WILD-TYPE 93 62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     14   11
  ARID2 WILD-TYPE   93   62
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             14              93
  YES            11              62
[1] 2 2
[1] FALSE
D7V9, binary
                 cls
clus                0   1
  ARID2 MUTATED     6  31
  ARID2 WILD-TYPE  31 222
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      6   31
  ARID2 WILD-TYPE   31  222
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO              6              31
  YES            31             222
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, binary
                 cls
clus                0   1
  ARID2 MUTATED    12  25
  ARID2 WILD-TYPE  97 156
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     12   25
  ARID2 WILD-TYPE   97  156
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            12              97
  MALE              25             156
[1] 2 2
[1] FALSE
D7V12, binary
                 cls
clus                0   1
  ARID2 MUTATED    32   5
  ARID2 WILD-TYPE 222  30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     32    5
  ARID2 WILD-TYPE  222   30
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             32             222
  YES             5              30
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED       0                         0    37
  ARID2 WILD-TYPE     5                         1   247
D7V13, multiclass
                           clus
vv                          ARID2 MUTATED ARID2 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                37             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"
D7V14, binary
                 cls
clus                0   1
  ARID2 MUTATED     1  36
  ARID2 WILD-TYPE   2 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   36
  ARID2 WILD-TYPE    2  247
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            36             247
[1] 2 2
[1] FALSE

Clustering(8) Variable = C15ORF23 MUTATION ANALYSIS
D8V1, survival
                    sevent
clus2                 0  1
  C15ORF23 MUTATED    6  5
  C15ORF23 WILD-TYPE 91 98
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                11                189 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 5                 98 
$`C15ORF23 MUTATED`
TCGA-EE-A2GD TCGA-D3-A51E TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29G TCGA-EE-A2A2 
      269.03       173.85        58.85        20.38        44.28        30.02 
TCGA-EE-A2MP TCGA-EE-A3J4 TCGA-FS-A1ZT TCGA-FS-A4F9 TCGA-GF-A4EO 
      227.01       111.85        35.28        13.28        18.25 

$`C15ORF23 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      134.40        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61       110.53        60.10        64.83        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       24.89         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14        12.99         0.26        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       346.49       185.19       115.43        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28        67.89        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67       173.19        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             13.28               0.00 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
            269.03             346.49 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             44.28              47.41 
[1] "13.3 - 269.0 (44.3)" "0.0 - 346.5 (47.4)" 
[1] "hr=" "1.7"
D8V2, survival
                    sevent
clus2                  0   1
  C15ORF23 MUTATED     9  10
  C15ORF23 WILD-TYPE 115 150
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                19                265 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                10                150 
$`C15ORF23 MUTATED`
TCGA-EE-A2GD TCGA-D3-A2JD TCGA-D3-A51E TCGA-D3-A5GO TCGA-DA-A1IC TCGA-EE-A181 
      340.14        11.87       174.84       137.92        68.09        33.73 
TCGA-EE-A29G TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3AH 
       72.07        59.64        67.43        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        34.03        19.43        15.78 
TCGA-GN-A266 
       10.13 

$`C15ORF23 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      115.53       168.00        86.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75        45.30        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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-D9-A6EC 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       40.60        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       78.97        13.97        63.78        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54        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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 
       28.77        54.51        13.81        41.59       172.18        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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41       148.80        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.02        77.82        66.67        28.73       174.84        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         2.04       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             10.13               0.20 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
            340.14             369.93 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             59.64              53.92 
[1] "10.1 - 340.1 (59.6)" "0.2 - 369.9 (53.9)" 
[1] "hr=" "1.3"
D8V3, continuous
                    vv
clus                 I/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      23       10       25       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C15ORF23 MUTATED           0         2         0         2          1
  C15ORF23 WILD-TYPE        10        12        10        34         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C15ORF23 MUTATED            2          4        0
  C15ORF23 WILD-TYPE         24         39       16
D8V4, multiclass
            clus
vv           C15ORF23 MUTATED C15ORF23 WILD-TYPE
  I/II NOS                  1                  9
  STAGE 0                   0                  6
  STAGE I                   2                 23
  STAGE IA                  0                 10
  STAGE IB                  0                 25
  STAGE II                  4                 14
  STAGE IIA                 0                 10
  STAGE IIB                 2                 12
  STAGE IIC                 0                 10
  STAGE III                 2                 34
  STAGE IIIA                1                 13
  STAGE IIIB                2                 24
  STAGE IIIC                4                 39
  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    52 58 55 48
D8V5, multiclass
       clus
vv      C15ORF23 MUTATED C15ORF23 WILD-TYPE
  T0+T1                1                 52
  T2                   4                 58
  T3                   5                 55
  T4                   7                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C15ORF23 MUTATED     9   4   2   2
  C15ORF23 WILD-TYPE 134  49  32  33
D8V6, multiclass
    clus
vv   C15ORF23 MUTATED C15ORF23 WILD-TYPE
  N0                9                134
  N1                4                 49
  N2                2                 32
  N3                2                 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"
D8V7, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED    17   0
  C15ORF23 WILD-TYPE 239  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED     17    0
  C15ORF23 WILD-TYPE  239   17
   clus
vv  C15ORF23 MUTATED C15ORF23 WILD-TYPE
  0               17                239
  1                0                 17
[1] 2 2
[1] FALSE
D8V8, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     5   6
  C15ORF23 WILD-TYPE 102  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      5    6
  C15ORF23 WILD-TYPE  102   67
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  NO                 5                102
  YES                6                 67
[1] 2 2
[1] FALSE
D8V9, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     3  16
  C15ORF23 WILD-TYPE  34 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      3   16
  C15ORF23 WILD-TYPE   34  237
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  NO                 3                 34
  YES               16                237
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     5  14
  C15ORF23 WILD-TYPE 104 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      5   14
  C15ORF23 WILD-TYPE  104  167
        clus
vv       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  FEMALE                5                104
  MALE                 14                167
[1] 2 2
[1] FALSE
D8V12, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED    16   3
  C15ORF23 WILD-TYPE 238  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED     16    3
  C15ORF23 WILD-TYPE  238   32
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  NO                16                238
  YES                3                 32
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C15ORF23 MUTATED       0                         0    19
  C15ORF23 WILD-TYPE     5                         1   265
D8V13, multiclass
                           clus
vv                          C15ORF23 MUTATED C15ORF23 WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   19                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"
D8V14, binary
                    cls
clus                   0   1
  C15ORF23 MUTATED     0  19
  C15ORF23 WILD-TYPE   3 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      0   19
  C15ORF23 WILD-TYPE    3  264
                        clus
vv                       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               19                264
[1] 2 2
[1] FALSE

Clustering(9) Variable = NUDT11 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     3   3
  NUDT11 WILD-TYPE  94 100
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               6              194 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               3              100 
$`NUDT11 MUTATED`
TCGA-D3-A3CF TCGA-D3-A51F TCGA-DA-A1I1 TCGA-ER-A199 TCGA-ER-A19M TCGA-GN-A262 
       24.53        30.67        68.68         7.82        59.84        53.29 

$`NUDT11 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
        9.34        90.21        23.67       173.85       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 
       22.29        69.21        22.85        76.34       138.67       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       34.45        10.49         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      184.60       150.12        99.06        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       18.25         1.91       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            7.82             0.00 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           68.68           346.49 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
          41.980           47.295 
[1] "7.8 - 68.7 (42.0)"  "0.0 - 346.5 (47.3)"
[1] "hr=" "1.5"
D9V2, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     3   5
  NUDT11 WILD-TYPE 121 155
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               8              276 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              155 
$`NUDT11 MUTATED`
TCGA-D3-A3CF TCGA-D3-A51F TCGA-DA-A1I1 TCGA-EE-A3AG TCGA-ER-A199 TCGA-ER-A19M 
       24.53        55.73       222.51        41.59         9.17        61.05 
TCGA-ER-A19T TCGA-GN-A262 
        8.88       139.89 

$`NUDT11 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51H 
        9.34       103.59        39.75        45.30       174.84        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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-A3AH 
      122.73        64.04        28.77        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
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 
      302.07       152.35         6.44       131.51        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        49.48       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.78       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            8.88             0.20 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
          222.51           369.93 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           48.66            53.97 
[1] "8.9 - 222.5 (48.7)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.2"
D9V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NUDT11 MUTATED          0       0       0        0        1        0
  NUDT11 WILD-TYPE       10       6      25       10       24       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  NUDT11 MUTATED           0         0         0         2          0
  NUDT11 WILD-TYPE        10        14        10        34         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  NUDT11 MUTATED            0          3        1
  NUDT11 WILD-TYPE         26         40       15
D9V4, multiclass
            clus
vv           NUDT11 MUTATED NUDT11 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 0               25
  STAGE IA                0               10
  STAGE IB                1               24
  STAGE II                0               18
  STAGE IIA               0               10
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               2               34
  STAGE IIIA              0               14
  STAGE IIIB              0               26
  STAGE IIIC              3               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
  NUDT11 MUTATED       2  1  0  4
  NUDT11 WILD-TYPE    51 61 60 51
D9V5, multiclass
       clus
vv      NUDT11 MUTATED NUDT11 WILD-TYPE
  T0+T1              2               51
  T2                 1               61
  T3                 0               60
  T4                 4               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NUDT11 MUTATED     1   1   2   3
  NUDT11 WILD-TYPE 142  52  32  32
D9V6, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  N0              1              142
  N1              1               52
  N2              2               32
  N3              3               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"
D9V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     6   1
  NUDT11 WILD-TYPE 250  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      6    1
  NUDT11 WILD-TYPE  250   16
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              6              250
  1              1               16
[1] 2 2
[1] FALSE
D9V8, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     2   3
  NUDT11 WILD-TYPE 105  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      2    3
  NUDT11 WILD-TYPE  105   70
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               2              105
  YES              3               70
[1] 2 2
[1] FALSE
D9V9, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     2   6
  NUDT11 WILD-TYPE  35 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      2    6
  NUDT11 WILD-TYPE   35  247
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               2               35
  YES              6              247
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     3   5
  NUDT11 WILD-TYPE 106 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      3    5
  NUDT11 WILD-TYPE  106  176
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              3              106
  MALE                5              176
[1] 2 2
[1] FALSE
D9V12, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     7   1
  NUDT11 WILD-TYPE 247  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      7    1
  NUDT11 WILD-TYPE  247   34
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               7              247
  YES              1               34
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED       0                         0     8
  NUDT11 WILD-TYPE     5                         1   276
D9V13, multiclass
                           clus
vv                          NUDT11 MUTATED NUDT11 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   8
  NUDT11 WILD-TYPE   3 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    8
  NUDT11 WILD-TYPE    3  275
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8              275
[1] 2 2
[1] FALSE

Clustering(10) Variable = ZFX MUTATION ANALYSIS
D10V1, survival
               sevent
clus2            0  1
  ZFX MUTATED    6  4
  ZFX WILD-TYPE 91 99
  ZFX MUTATED ZFX WILD-TYPE 
           10           190 
  ZFX MUTATED ZFX WILD-TYPE 
            4            99 
$`ZFX MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-ER-A42L TCGA-FS-A1ZT 
       62.07        52.90         0.20        63.25        74.47        35.28 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-OD-A75X TCGA-QB-A6FS 
       23.21         3.06       297.01         7.23 

$`ZFX WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       38.76        33.24        31.96       166.75       269.03       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       27.35        19.04        36.85         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       32.05         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       36.33        78.61       130.95       136.27         4.47         5.29 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92         0.20         0.33 

  ZFX MUTATED ZFX WILD-TYPE 
          0.2           0.0 
  ZFX MUTATED ZFX WILD-TYPE 
       297.01        346.49 
  ZFX MUTATED ZFX WILD-TYPE 
       44.090        47.295 
[1] "0.2 - 297.0 (44.1)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.3"
D10V2, survival
               sevent
clus2             0   1
  ZFX MUTATED     8   7
  ZFX WILD-TYPE 116 153
  ZFX MUTATED ZFX WILD-TYPE 
           15           269 
  ZFX MUTATED ZFX WILD-TYPE 
            7           153 
$`ZFX MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GO TCGA-DA-A1I0 TCGA-EE-A17Z TCGA-EE-A2GC TCGA-EE-A2GR 
       62.07       126.81        20.38         8.65        67.43        42.77 
TCGA-EE-A2GT TCGA-EE-A2MJ TCGA-EE-A3JA TCGA-ER-A42L TCGA-FS-A1ZT TCGA-FS-A1ZW 
       44.88        96.23        53.19       149.03        53.16        49.48 
TCGA-FS-A1ZZ TCGA-OD-A75X TCGA-QB-A6FS 
       27.02       297.90         7.23 

$`ZFX WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
        7.04        36.46        29.82        27.22        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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-A2GE 
      115.96        59.64        39.29        86.14        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
      102.12        13.91        81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       12.95        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
      148.80        26.56        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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13         0.20         0.33         0.69 

  ZFX MUTATED ZFX WILD-TYPE 
         7.23          0.20 
  ZFX MUTATED ZFX WILD-TYPE 
       297.90        369.93 
  ZFX MUTATED ZFX WILD-TYPE 
        53.16         54.41 
[1] "7.2 - 297.9 (53.2)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.2"
D10V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ZFX MUTATED          0       0       0        1        1        3         1
  ZFX WILD-TYPE       10       6      25        9       24       15         9
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZFX MUTATED           3         0         2          0          1          1
  ZFX WILD-TYPE        11        10        34         14         25         42
               vv
clus            STAGE IV
  ZFX MUTATED          1
  ZFX WILD-TYPE       15
D10V4, multiclass
            clus
vv           ZFX MUTATED ZFX WILD-TYPE
  I/II NOS             0            10
  STAGE 0              0             6
  STAGE I              0            25
  STAGE IA             1             9
  STAGE IB             1            24
  STAGE II             3            15
  STAGE IIA            1             9
  STAGE IIB            3            11
  STAGE IIC            0            10
  STAGE III            2            34
  STAGE IIIA           0            14
  STAGE IIIB           1            25
  STAGE IIIC           1            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
  ZFX MUTATED       2  3  5  4
  ZFX WILD-TYPE    51 59 55 51
D10V5, multiclass
       clus
vv      ZFX MUTATED ZFX WILD-TYPE
  T0+T1           2            51
  T2              3            59
  T3              5            55
  T4              4            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  ZFX MUTATED    10   2   0   2
  ZFX WILD-TYPE 133  51  34  33
D10V6, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  N0          10           133
  N1           2            51
  N2           0            34
  N3           2            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"
D10V7, binary
               cls
clus              0   1
  ZFX MUTATED    14   1
  ZFX WILD-TYPE 242  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     14    1
  ZFX WILD-TYPE  242   16
   clus
vv  ZFX MUTATED ZFX WILD-TYPE
  0          14           242
  1           1            16
[1] 2 2
[1] FALSE
D10V8, binary
               cls
clus              0   1
  ZFX MUTATED     7   4
  ZFX WILD-TYPE 100  69
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      7    4
  ZFX WILD-TYPE  100   69
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO            7           100
  YES           4            69
[1] 2 2
[1] FALSE
D10V9, binary
               cls
clus              0   1
  ZFX MUTATED     1  14
  ZFX WILD-TYPE  36 239
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      1   14
  ZFX WILD-TYPE   36  239
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO            1            36
  YES          14           239
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, binary
               cls
clus              0   1
  ZFX MUTATED     2  13
  ZFX WILD-TYPE 107 168
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      2   13
  ZFX WILD-TYPE  107  168
        clus
vv       ZFX MUTATED ZFX WILD-TYPE
  FEMALE           2           107
  MALE            13           168
[1] 2 2
[1] FALSE
D10V12, binary
               cls
clus              0   1
  ZFX MUTATED    14   1
  ZFX WILD-TYPE 240  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     14    1
  ZFX WILD-TYPE  240   34
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO           14           240
  YES           1            34
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFX MUTATED       0                         0    15
  ZFX WILD-TYPE     5                         1   269
D10V13, multiclass
                           clus
vv                          ZFX MUTATED ZFX WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              15           269
[1] 3 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
  ZFX MUTATED     1  14
  ZFX WILD-TYPE   2 269
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      1   14
  ZFX WILD-TYPE    2  269
                        clus
vv                       ZFX MUTATED ZFX WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          14           269
[1] 2 2
[1] FALSE

Clustering(11) Variable = SLC38A4 MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  SLC38A4 MUTATED   15  7
  SLC38A4 WILD-TYPE 82 96
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               22               178 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
                7                96 
$`SLC38A4 MUTATED`
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A51T TCGA-DA-A1I1 
       62.07       166.75        27.35        36.85        11.34        68.68 
TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2A2 
       58.85         3.91        20.38        75.55        47.74        30.02 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19A TCGA-GF-A4EO 
      171.85        63.25       143.93        23.51         4.54        18.25 
TCGA-GN-A265 TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A693 
       96.92        46.92         7.23         0.33 

$`SLC38A4 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       38.76        33.24        31.96       269.03        52.90       134.40 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
      173.85        30.67       144.46        31.76        62.70        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       45.70       177.86        15.02        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67       150.61       110.53        60.10        64.83 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       30.44       225.11        42.64        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B 
       13.15        24.89         0.00        26.24        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       76.14        12.99         0.26        44.28        47.41        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       346.49       185.19       115.43        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK 
       15.25         5.75        23.77       209.79        94.19        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      104.78       145.45       227.01        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       10.49         7.82        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        1.91        53.29       117.93        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-OD-A75X TCGA-RP-A690 
      120.53        34.49       297.01         0.20 

  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
             0.33              0.00 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           171.85            346.49 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           41.885            48.380 
[1] "0.3 - 171.8 (41.9)" "0.0 - 346.5 (48.4)"
[1] "hr=" "1.3"
D11V2, survival
                   sevent
clus2                 0   1
  SLC38A4 MUTATED    19  14
  SLC38A4 WILD-TYPE 105 146
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               33               251 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
               14               146 
$`SLC38A4 MUTATED`
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JD TCGA-D3-A2JK 
       62.07       168.26        27.35        36.95        11.87        12.10 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A1JW TCGA-DA-A1I1 TCGA-DA-A1IC TCGA-EB-A44Q 
       26.89       137.92         3.65       222.51        68.09        13.87 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2A2 
       33.73       151.27        63.35        56.84        46.82        59.64 
TCGA-EE-A2GI TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 
       48.72       204.66        96.23       162.48        71.21        36.95 
TCGA-EE-A3JA TCGA-ER-A19A TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
       53.19        77.75        19.43        15.78        96.92        10.13 
TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A693 
       48.89         7.23         0.33 

$`SLC38A4 WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 
        2.60       340.14       126.81       134.40        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08       171.58        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
       40.60        33.93        10.49       225.96        43.36        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        14.70        26.89         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        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       61.28       369.93        25.87       195.02        17.92       115.96 
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       173.79       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65        43.23        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        64.08        34.32       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      152.81        35.44        13.94         9.17        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       13.51        19.30         9.90         2.04       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A694 
       10.42        22.13       297.90         0.20         0.69 

  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
             0.33              0.20 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
           222.51            369.93 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
            48.89             54.41 
[1] "0.3 - 222.5 (48.9)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.2"
D11V3, continuous
                   vv
clus                I/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      24        8       22       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SLC38A4 MUTATED           1         1         0         5          1
  SLC38A4 WILD-TYPE         9        13        10        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC38A4 MUTATED            2          7        2
  SLC38A4 WILD-TYPE         24         36       14
D11V4, multiclass
            clus
vv           SLC38A4 MUTATED SLC38A4 WILD-TYPE
  I/II NOS                 0                10
  STAGE 0                  1                 5
  STAGE I                  1                24
  STAGE IA                 2                 8
  STAGE IB                 3                22
  STAGE II                 3                15
  STAGE IIA                1                 9
  STAGE IIB                1                13
  STAGE IIC                0                10
  STAGE III                5                31
  STAGE IIIA               1                13
  STAGE IIIB               2                24
  STAGE IIIC               7                36
  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  8
  SLC38A4 WILD-TYPE    47 58 55 47
D11V5, multiclass
       clus
vv      SLC38A4 MUTATED SLC38A4 WILD-TYPE
  T0+T1               6                47
  T2                  4                58
  T3                  5                55
  T4                  8                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC38A4 MUTATED    14   5   6   3
  SLC38A4 WILD-TYPE 129  48  28  32
D11V6, multiclass
    clus
vv   SLC38A4 MUTATED SLC38A4 WILD-TYPE
  N0              14               129
  N1               5                48
  N2               6                28
  N3               3                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"
D11V7, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED    27   2
  SLC38A4 WILD-TYPE 229  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED     27    2
  SLC38A4 WILD-TYPE  229   15
   clus
vv  SLC38A4 MUTATED SLC38A4 WILD-TYPE
  0              27               229
  1               2                15
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                 0  1
  SLC38A4 MUTATED   12  5
  SLC38A4 WILD-TYPE 95 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED     12    5
  SLC38A4 WILD-TYPE   95   68
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  NO               12                95
  YES               5                68
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     9  24
  SLC38A4 WILD-TYPE  28 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      9   24
  SLC38A4 WILD-TYPE   28  229
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  NO                9                28
  YES              24               229
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     6  27
  SLC38A4 WILD-TYPE 103 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      6   27
  SLC38A4 WILD-TYPE  103  154
        clus
vv       SLC38A4 MUTATED SLC38A4 WILD-TYPE
  FEMALE               6               103
  MALE                27               154
[1] 2 2
[1] FALSE
D11V12, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED    27   6
  SLC38A4 WILD-TYPE 227  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED     27    6
  SLC38A4 WILD-TYPE  227   29
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  NO               27               227
  YES               6                29
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC38A4 MUTATED       1                         0    32
  SLC38A4 WILD-TYPE     4                         1   252
D11V13, multiclass
                           clus
vv                          SLC38A4 MUTATED SLC38A4 WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  32               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"
D11V14, binary
                   cls
clus                  0   1
  SLC38A4 MUTATED     0  32
  SLC38A4 WILD-TYPE   3 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      0   32
  SLC38A4 WILD-TYPE    3  251
                        clus
vv                       SLC38A4 MUTATED SLC38A4 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              32               251
[1] 2 2
[1] FALSE

Clustering(12) Variable = FAM58A MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  FAM58A MUTATED     2   2
  FAM58A WILD-TYPE  95 101
  FAM58A MUTATED FAM58A WILD-TYPE 
               4              196 
  FAM58A MUTATED FAM58A WILD-TYPE 
               2              101 
$`FAM58A MUTATED`
TCGA-EE-A3JD TCGA-DA-A1IC TCGA-EE-A2MT TCGA-GN-A4U8 
       27.35        58.85        23.51        46.92 

$`FAM58A WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 
       68.68       150.61       110.53        60.10        64.83        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      104.78       145.45       227.01       143.93        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  FAM58A MUTATED FAM58A WILD-TYPE 
           23.51             0.00 
  FAM58A MUTATED FAM58A WILD-TYPE 
           58.85           346.49 
  FAM58A MUTATED FAM58A WILD-TYPE 
          37.135           47.575 
[1] "23.5 - 58.9 (37.1)" "0.0 - 346.5 (47.6)"
[1] "hr=" "1.7"
D12V2, survival
                  sevent
clus2                0   1
  FAM58A MUTATED     2   4
  FAM58A WILD-TYPE 122 156
  FAM58A MUTATED FAM58A WILD-TYPE 
               6              278 
  FAM58A MUTATED FAM58A WILD-TYPE 
               4              156 
$`FAM58A MUTATED`
TCGA-EE-A3JD TCGA-DA-A1IC TCGA-EE-A29N TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-GN-A4U8 
       27.35        68.09        18.61        71.21        36.95        48.89 

$`FAM58A WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       88.87        53.92        65.92        40.60        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        56.84        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23       162.48        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       39.35        10.42        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  FAM58A MUTATED FAM58A WILD-TYPE 
           18.61             0.20 
  FAM58A MUTATED FAM58A WILD-TYPE 
           71.21           369.93 
  FAM58A MUTATED FAM58A WILD-TYPE 
          42.920           54.215 
[1] "18.6 - 71.2 (42.9)" "0.2 - 369.9 (54.2)"
[1] "hr=" "1.7"
D12V3, continuous
                  vv
clus               I/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      25       10       24       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  FAM58A MUTATED           0         0         0         2          0
  FAM58A WILD-TYPE        10        14        10        34         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  FAM58A MUTATED            1          0        0
  FAM58A WILD-TYPE         25         43       16
D12V4, multiclass
            clus
vv           FAM58A MUTATED FAM58A WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 0                6
  STAGE I                 0               25
  STAGE IA                0               10
  STAGE IB                1               24
  STAGE II                0               18
  STAGE IIA               0               10
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               2               34
  STAGE IIIA              0               14
  STAGE IIIB              1               25
  STAGE IIIC              0               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
  FAM58A MUTATED       0  1  1  1
  FAM58A WILD-TYPE    53 61 59 54
D12V5, multiclass
       clus
vv      FAM58A MUTATED FAM58A WILD-TYPE
  T0+T1              0               53
  T2                 1               61
  T3                 1               59
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM58A MUTATED     2   1   2   0
  FAM58A WILD-TYPE 141  52  32  35
D12V6, multiclass
    clus
vv   FAM58A MUTATED FAM58A WILD-TYPE
  N0              2              141
  N1              1               52
  N2              2               32
  N3              0               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"
D12V7, binary
                  cls
clus                 0   1
  FAM58A MUTATED     5   0
  FAM58A WILD-TYPE 251  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      5    0
  FAM58A WILD-TYPE  251   17
   clus
vv  FAM58A MUTATED FAM58A WILD-TYPE
  0              5              251
  1              0               17
[1] 2 2
[1] FALSE
D12V8, binary
                  cls
clus                 0   1
  FAM58A MUTATED     3   0
  FAM58A WILD-TYPE 104  73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      3    0
  FAM58A WILD-TYPE  104   73
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  NO               3              104
  YES              0               73
[1] 2 2
[1] FALSE
D12V9, binary
                  cls
clus                 0   1
  FAM58A MUTATED     1   5
  FAM58A WILD-TYPE  36 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      1    5
  FAM58A WILD-TYPE   36  248
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  NO               1               36
  YES              5              248
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, binary
                  cls
clus                 0   1
  FAM58A MUTATED     0   6
  FAM58A WILD-TYPE 109 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      0    6
  FAM58A WILD-TYPE  109  175
        clus
vv       FAM58A MUTATED FAM58A WILD-TYPE
  FEMALE              0              109
  MALE                6              175
[1] 2 2
[1] FALSE
D12V12, binary
                  cls
clus                 0   1
  FAM58A MUTATED     4   2
  FAM58A WILD-TYPE 250  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      4    2
  FAM58A WILD-TYPE  250   33
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  NO               4              250
  YES              2               33
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM58A MUTATED       0                         0     6
  FAM58A WILD-TYPE     5                         1   278
D12V13, multiclass
                           clus
vv                          FAM58A MUTATED FAM58A WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  6              278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                  cls
clus                 0   1
  FAM58A MUTATED     0   6
  FAM58A WILD-TYPE   3 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      0    6
  FAM58A WILD-TYPE    3  277
                        clus
vv                       FAM58A MUTATED FAM58A WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              6              277
[1] 2 2
[1] FALSE

Clustering(13) Variable = PPP6C MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  PPP6C MUTATED   10  6
  PPP6C WILD-TYPE 87 97
  PPP6C MUTATED PPP6C WILD-TYPE 
             16             184 
  PPP6C MUTATED PPP6C WILD-TYPE 
              6              97 
$`PPP6C MUTATED`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A2GD TCGA-FW-A3R5 TCGA-D9-A6EC TCGA-DA-A1I1 
       38.76        33.24       269.03        36.85        69.21        68.68 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A29W TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2ML 
      225.11        42.64       185.19        18.35       103.13       104.78 
TCGA-EE-A3JI TCGA-FS-A1ZC TCGA-FS-A1ZW TCGA-GN-A267 
      135.98       312.07        23.21        17.06 

$`PPP6C WILD-TYPE`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       62.07        31.96       166.75        52.90       134.40        27.35 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG 
       42.05        45.70       177.86        15.02        22.29        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       58.85        30.44         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 
       47.41        47.74        27.16        61.12       346.49       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
      171.85        63.25        89.26       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      168.85        19.86        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      136.27        35.28         4.47         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       96.92        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  PPP6C MUTATED PPP6C WILD-TYPE 
          17.06            0.00 
  PPP6C MUTATED PPP6C WILD-TYPE 
         312.07          346.49 
  PPP6C MUTATED PPP6C WILD-TYPE 
         68.945          47.050 
[1] "17.1 - 312.1 (68.9)" "0.0 - 346.5 (47.0)" 
[1] "hr=" "2.6"
D13V2, survival
                 sevent
clus2               0   1
  PPP6C MUTATED    12   8
  PPP6C WILD-TYPE 112 152
  PPP6C MUTATED PPP6C WILD-TYPE 
             20             264 
  PPP6C MUTATED PPP6C WILD-TYPE 
              8             152 
$`PPP6C MUTATED`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A29L TCGA-EE-A2GD TCGA-FW-A3R5 TCGA-D3-A3MV 
       46.32        68.25         2.60       340.14        36.95        45.30 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A29R TCGA-EE-A29W 
       77.56       222.51       225.96        43.36        14.47       195.02 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A3JI TCGA-FS-A1ZC TCGA-FS-A1ZH 
       75.48       129.27       216.66       152.81       357.37        32.75 
TCGA-FS-A1ZW TCGA-GN-A267 
       49.48        64.44 

$`PPP6C WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       62.07        13.87        54.02        94.98        68.15       168.26 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      126.81       134.40        27.35        31.40        50.76        15.45 
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        66.48        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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       60.23        24.53         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-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29         9.90        25.18        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       64.64        56.84        18.61        56.42        66.74        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      369.93        25.87        17.92        46.82       115.96        59.64 
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       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       48.72       107.38        54.74        79.66       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
       42.77        81.21        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-A2MM TCGA-EE-A2MN 
       16.96       204.66        96.23       180.39       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        64.04        28.77        54.51        13.81        41.59 
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-ER-A195 TCGA-ER-A197 
       53.19       201.80        51.35       134.33        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       48.85        53.52        46.45         9.70        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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       15.78       139.89       117.93        96.92        10.13        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  PPP6C MUTATED PPP6C WILD-TYPE 
            2.6             0.2 
  PPP6C MUTATED PPP6C WILD-TYPE 
         357.37          369.93 
  PPP6C MUTATED PPP6C WILD-TYPE 
         71.865          53.390 
[1] "2.6 - 357.4 (71.9)" "0.2 - 369.9 (53.4)"
[1] "hr=" "2.6"
D13V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PPP6C MUTATED          1       1       3        0        0        1         0
  PPP6C WILD-TYPE        9       5      22       10       25       17        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PPP6C MUTATED           1         1         2          2          3
  PPP6C WILD-TYPE        13         9        34         12         23
                 vv
clus              STAGE IIIC STAGE IV
  PPP6C MUTATED            3        1
  PPP6C WILD-TYPE         40       15
D13V4, multiclass
            clus
vv           PPP6C MUTATED PPP6C WILD-TYPE
  I/II NOS               1               9
  STAGE 0                1               5
  STAGE I                3              22
  STAGE IA               0              10
  STAGE IB               0              25
  STAGE II               1              17
  STAGE IIA              0              10
  STAGE IIB              1              13
  STAGE IIC              1               9
  STAGE III              2              34
  STAGE IIIA             2              12
  STAGE IIIB             3              23
  STAGE IIIC             3              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
  PPP6C MUTATED       3  4  4  4
  PPP6C WILD-TYPE    50 58 56 51
D13V5, multiclass
       clus
vv      PPP6C MUTATED PPP6C WILD-TYPE
  T0+T1             3              50
  T2                4              58
  T3                4              56
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PPP6C MUTATED     8   4   5   2
  PPP6C WILD-TYPE 135  49  29  33
D13V6, multiclass
    clus
vv   PPP6C MUTATED PPP6C WILD-TYPE
  N0             8             135
  N1             4              49
  N2             5              29
  N3             2              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"
D13V7, binary
                 cls
clus                0   1
  PPP6C MUTATED    18   1
  PPP6C WILD-TYPE 238  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED     18    1
  PPP6C WILD-TYPE  238   16
   clus
vv  PPP6C MUTATED PPP6C WILD-TYPE
  0            18             238
  1             1              16
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus                0   1
  PPP6C MUTATED     7   7
  PPP6C WILD-TYPE 100  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      7    7
  PPP6C WILD-TYPE  100   66
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  NO              7             100
  YES             7              66
[1] 2 2
[1] FALSE
D13V9, binary
                 cls
clus                0   1
  PPP6C MUTATED     1  19
  PPP6C WILD-TYPE  36 234
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      1   19
  PPP6C WILD-TYPE   36  234
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  NO              1              36
  YES            19             234
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, binary
                 cls
clus                0   1
  PPP6C MUTATED     7  13
  PPP6C WILD-TYPE 102 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      7   13
  PPP6C WILD-TYPE  102  168
        clus
vv       PPP6C MUTATED PPP6C WILD-TYPE
  FEMALE             7             102
  MALE              13             168
[1] 2 2
[1] FALSE
D13V12, binary
                 cls
clus                0   1
  PPP6C MUTATED    17   3
  PPP6C WILD-TYPE 237  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED     17    3
  PPP6C WILD-TYPE  237   32
     clus
vv    PPP6C MUTATED PPP6C WILD-TYPE
  NO             17             237
  YES             3              32
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP6C MUTATED       0                         0    20
  PPP6C WILD-TYPE     5                         1   264
D13V13, multiclass
                           clus
vv                          PPP6C MUTATED PPP6C WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                20             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"
D13V14, binary
                 cls
clus                0   1
  PPP6C MUTATED     0  20
  PPP6C WILD-TYPE   3 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      0   20
  PPP6C WILD-TYPE    3  263
                        clus
vv                       PPP6C MUTATED PPP6C WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            20             263
[1] 2 2
[1] FALSE

Clustering(14) Variable = C7ORF58 MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  C7ORF58 MUTATED   15 11
  C7ORF58 WILD-TYPE 82 92
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               26               174 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               11                92 
$`C7ORF58 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q4 
       52.90       134.40        27.35        19.04        36.85        31.89 
TCGA-DA-A1HV TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2GU 
       76.34         0.26        27.16        26.14         0.76        81.99 
TCGA-EE-A2M7 TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 
       15.25       124.31        54.51         6.28       111.85        45.90 
TCGA-ER-A42L TCGA-FS-A1ZC TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
       74.47       312.07        17.06        42.48         7.59       120.53 
TCGA-OD-A75X TCGA-RP-A693 
      297.01         0.33 

$`C7ORF58 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.42        15.72       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
      177.86        15.02        22.29        69.21        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       75.55        79.20        75.22        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M6 
       32.48        18.35        93.63         0.20        71.31       103.13 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J8 
       53.26       122.73        64.04         4.41        67.89         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        32.05         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A690 
      117.93        96.92        34.49        46.92         7.23         0.20 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             0.26              0.00 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           312.07            346.49 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           39.665            48.545 
[1] "0.3 - 312.1 (39.7)" "0.0 - 346.5 (48.5)"
[1] "hr=" "1.3"
D14V2, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    19  17
  C7ORF58 WILD-TYPE 105 143
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               36               248 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               17               143 
$`C7ORF58 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 
      126.81       134.40        27.35        31.40        50.76        36.95 
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        76.57        20.38 
TCGA-DA-A3F3 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2GU 
       10.49        63.78        56.42        59.28        13.91        94.82 
TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
       28.83        47.28       124.31        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-ER-A42L TCGA-FS-A1ZC TCGA-FS-A4FB TCGA-GF-A6C9 
      127.20        64.08       149.03       357.37        26.73        15.78 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-OD-A75X TCGA-RP-A693 
       64.44        62.79        32.48       121.91       297.90         0.33 

$`C7ORF58 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-FS-A1ZF TCGA-D3-A1Q1 
       68.15       168.26         2.60       340.14        15.45        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.57        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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW 
      135.75       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 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        36.03       144.89       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       33.93       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       13.97        72.07        64.64        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC 
       46.82       115.96        59.64        39.29        86.14        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       75.48       102.12        42.77        81.21        44.88        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
      129.27        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       180.39       216.66       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-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      122.73        64.04        28.77        41.59       172.18        36.95 
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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21        12.95        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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85        53.52        46.45         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        34.03        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       19.43         2.04       139.89       117.93        96.92        10.13 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       48.00        39.35        10.42        48.89        22.13         7.23 
TCGA-RP-A690 TCGA-RP-A694 
        0.20         0.69 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             0.33              0.20 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           357.37            369.93 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           57.850            53.225 
[1] "0.3 - 357.4 (57.9)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.4"
D14V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C7ORF58 MUTATED          2       0       2        2        0        7
  C7ORF58 WILD-TYPE        8       6      23        8       25       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C7ORF58 MUTATED           0         2         1         6          2
  C7ORF58 WILD-TYPE        10        12         9        30         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C7ORF58 MUTATED            6          2        2
  C7ORF58 WILD-TYPE         20         41       14
D14V4, multiclass
            clus
vv           C7ORF58 MUTATED C7ORF58 WILD-TYPE
  I/II NOS                 2                 8
  STAGE 0                  0                 6
  STAGE I                  2                23
  STAGE IA                 2                 8
  STAGE IB                 0                25
  STAGE II                 7                11
  STAGE IIA                0                10
  STAGE IIB                2                12
  STAGE IIC                1                 9
  STAGE III                6                30
  STAGE IIIA               2                12
  STAGE IIIB               6                20
  STAGE IIIC               2                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
  C7ORF58 MUTATED       7  6 10  6
  C7ORF58 WILD-TYPE    46 56 50 49
D14V5, multiclass
       clus
vv      C7ORF58 MUTATED C7ORF58 WILD-TYPE
  T0+T1               7                46
  T2                  6                56
  T3                 10                50
  T4                  6                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C7ORF58 MUTATED    16  10   5   2
  C7ORF58 WILD-TYPE 127  43  29  33
D14V6, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  N0              16               127
  N1              10                43
  N2               5                29
  N3               2                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"
D14V7, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    34   2
  C7ORF58 WILD-TYPE 222  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     34    2
  C7ORF58 WILD-TYPE  222   15
   clus
vv  C7ORF58 MUTATED C7ORF58 WILD-TYPE
  0              34               222
  1               2                15
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  C7ORF58 MUTATED   13  9
  C7ORF58 WILD-TYPE 94 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     13    9
  C7ORF58 WILD-TYPE   94   64
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO               13                94
  YES               9                64
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     8  29
  C7ORF58 WILD-TYPE  29 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      8   29
  C7ORF58 WILD-TYPE   29  224
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO                8                29
  YES              29               224
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    13  24
  C7ORF58 WILD-TYPE  96 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     13   24
  C7ORF58 WILD-TYPE   96  157
        clus
vv       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  FEMALE              13                96
  MALE                24               157
[1] 2 2
[1] FALSE
D14V12, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    32   5
  C7ORF58 WILD-TYPE 222  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     32    5
  C7ORF58 WILD-TYPE  222   30
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO               32               222
  YES               5                30
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C7ORF58 MUTATED       0                         0    37
  C7ORF58 WILD-TYPE     5                         1   247
D14V13, multiclass
                           clus
vv                          C7ORF58 MUTATED C7ORF58 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  37               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"
D14V14, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     0  37
  C7ORF58 WILD-TYPE   3 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      0   37
  C7ORF58 WILD-TYPE    3  246
                        clus
vv                       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              37               246
[1] 2 2
[1] FALSE

Clustering(15) Variable = COL3A1 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2               0  1
  COL3A1 MUTATED   18 17
  COL3A1 WILD-TYPE 79 86
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              35              165 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              17               86 
$`COL3A1 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q6 
       52.90       134.40        27.35        19.04        36.85        49.35 
TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A5GN TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I1 
       86.30        66.08        45.70        69.21       138.67        68.68 
TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E 
      225.11        13.15        24.89        20.38        12.99         0.26 
TCGA-EE-A2GP TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
        0.76        23.77        63.25       143.93        23.51        64.04 
TCGA-EE-A3JB TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A2NC TCGA-ER-A42L TCGA-FS-A1Z3 
      168.85        39.81       150.12        22.36        74.47         8.35 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GN-A4U4 TCGA-OD-A75X TCGA-RP-A693 
       13.28        55.59        34.49       297.01         0.33 

$`COL3A1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.42        15.72        31.89       110.93       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      168.00       107.61        36.30       171.58        64.83        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       62.70        11.34        42.05       177.86        15.02        22.29 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.85        76.34       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       58.85        30.44        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       18.21         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       76.14        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75       209.79        94.19       171.85        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      145.45       227.01        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       53.29        11.47       184.60        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      120.76        49.71        47.18       146.63        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       32.05         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD 
        5.29         3.06        18.51        66.67       173.19        80.68 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A690 
       46.92         7.23         0.20 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            0.26             0.00 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          297.01           346.49 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
           45.70            47.41 
[1] "0.3 - 297.0 (45.7)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1"  
D15V2, survival
                  sevent
clus2                0   1
  COL3A1 MUTATED    27  31
  COL3A1 WILD-TYPE  97 129
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              58              226 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              31              129 
$`COL3A1 MUTATED`
TCGA-D3-A3ML TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       13.87         2.60       126.81       134.40        27.35        31.40 
TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A2JO 
       36.95        71.80        86.76        11.87        12.10        66.08 
TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D9-A1JW 
       46.98        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 
       77.56       144.89       222.51       225.96        29.82        27.22 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI 
       33.73        13.97        63.78        39.29        67.43        48.72 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT 
       13.91        21.67        61.51        96.23       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JE 
       64.04        41.59       138.81        36.95       201.80        51.35 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A2NC TCGA-ER-A42L 
       48.89        26.37       152.35         6.44        43.82       149.03 
TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A6C9 
       20.91        23.93        28.73        34.03        55.59        15.78 
TCGA-GN-A266 TCGA-GN-A4U4 TCGA-OD-A75X TCGA-RP-A693 
       10.13        39.35       297.90         0.33 

$`COL3A1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      168.26       340.14        50.76        15.45        16.57        16.67 
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-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-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP 
      168.00       113.52        42.08       171.58        66.48        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        58.06       166.52        86.93        60.23        24.53 
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-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 
      178.32       125.19       151.53        54.67         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29         9.90        25.18        22.95        76.57        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       65.92        40.60        68.09        33.93        10.49        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       36.46         8.65        14.70        26.89         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        85.08        78.97 
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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       46.82       115.96        59.64        86.14        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82       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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       43.23        53.26       124.31       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       13.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M 
       98.40        12.59        13.02       302.07       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      105.07        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        93.01        46.98        33.21        12.95        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         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 
       54.41        80.68        17.46        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.43         2.04       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 
       62.79        32.48        48.00       121.91        10.42        48.89 
TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A694 
       22.13         7.23         0.20         0.69 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            0.33             0.20 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          297.90           369.93 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          44.560           55.235 
[1] "0.3 - 297.9 (44.6)" "0.2 - 369.9 (55.2)"
[1] "hr=" "1.1"
D15V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  COL3A1 MUTATED          0       0       6        2        4        7
  COL3A1 WILD-TYPE       10       6      19        8       21       11
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  COL3A1 MUTATED           1         2         0        12          2
  COL3A1 WILD-TYPE         9        12        10        24         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  COL3A1 MUTATED            7          6        4
  COL3A1 WILD-TYPE         19         37       12
D15V4, multiclass
            clus
vv           COL3A1 MUTATED COL3A1 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 6               19
  STAGE IA                2                8
  STAGE IB                4               21
  STAGE II                7               11
  STAGE IIA               1                9
  STAGE IIB               2               12
  STAGE IIC               0               10
  STAGE III              12               24
  STAGE IIIA              2               12
  STAGE IIIB              7               19
  STAGE IIIC              6               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 11 15 10
  COL3A1 WILD-TYPE    42 51 45 45
D15V5, multiclass
       clus
vv      COL3A1 MUTATED COL3A1 WILD-TYPE
  T0+T1             11               42
  T2                11               51
  T3                15               45
  T4                10               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  COL3A1 MUTATED    24  14  10   4
  COL3A1 WILD-TYPE 119  39  24  31
D15V6, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  N0             24              119
  N1             14               39
  N2             10               24
  N3              4               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"
D15V7, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    52   4
  COL3A1 WILD-TYPE 204  13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     52    4
  COL3A1 WILD-TYPE  204   13
   clus
vv  COL3A1 MUTATED COL3A1 WILD-TYPE
  0             52              204
  1              4               13
[1] 2 2
[1] FALSE
D15V8, binary
                  cls
clus                0  1
  COL3A1 MUTATED   22 13
  COL3A1 WILD-TYPE 85 60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     22   13
  COL3A1 WILD-TYPE   85   60
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO              22               85
  YES             13               60
[1] 2 2
[1] FALSE
D15V9, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    11  48
  COL3A1 WILD-TYPE  26 205
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     11   48
  COL3A1 WILD-TYPE   26  205
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO              11               26
  YES             48              205
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    11  48
  COL3A1 WILD-TYPE  98 133
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     11   48
  COL3A1 WILD-TYPE   98  133
        clus
vv       COL3A1 MUTATED COL3A1 WILD-TYPE
  FEMALE             11               98
  MALE               48              133
[1] 2 2
[1] FALSE
D15V12, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    53   6
  COL3A1 WILD-TYPE 201  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     53    6
  COL3A1 WILD-TYPE  201   29
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO              53              201
  YES              6               29
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL3A1 MUTATED       1                         0    58
  COL3A1 WILD-TYPE     4                         1   226
D15V13, multiclass
                           clus
vv                          COL3A1 MUTATED COL3A1 WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 58              226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                  cls
clus                 0   1
  COL3A1 MUTATED     0  57
  COL3A1 WILD-TYPE   3 226
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED      0   57
  COL3A1 WILD-TYPE    3  226
                        clus
vv                       COL3A1 MUTATED COL3A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             57              226
[1] 2 2
[1] FALSE

Clustering(16) Variable = CDK4 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  CDK4 MUTATED     2   3
  CDK4 WILD-TYPE  95 100
  CDK4 MUTATED CDK4 WILD-TYPE 
             5            195 
  CDK4 MUTATED CDK4 WILD-TYPE 
             3            100 
$`CDK4 MUTATED`
TCGA-D3-A2JA TCGA-EE-A2MG TCGA-EE-A3AD TCGA-ER-A19W TCGA-GF-A6C8 
       15.75        94.19         4.41       146.63         1.91 

$`CDK4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB 
       76.41        62.60        25.64        45.99        62.86       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        5.75        23.77       209.79       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73        64.04        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      120.76        49.71        47.18        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90        18.25        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  CDK4 MUTATED CDK4 WILD-TYPE 
          1.91           0.00 
  CDK4 MUTATED CDK4 WILD-TYPE 
        146.63         346.49 
  CDK4 MUTATED CDK4 WILD-TYPE 
         15.75          47.41 
[1] "1.9 - 146.6 (15.8)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.6"
D16V2, survival
                sevent
clus2              0   1
  CDK4 MUTATED     2   6
  CDK4 WILD-TYPE 122 154
  CDK4 MUTATED CDK4 WILD-TYPE 
             8            276 
  CDK4 MUTATED CDK4 WILD-TYPE 
             6            154 
$`CDK4 MUTATED`
TCGA-D3-A2JA TCGA-EB-A44R TCGA-EE-A29V TCGA-EE-A2MG TCGA-EE-A3AD TCGA-ER-A19E 
      115.53        10.36        25.87       103.20        28.77        13.02 
TCGA-ER-A19W TCGA-GF-A6C8 
      148.18         2.04 

$`CDK4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       10.49       225.96        43.36        13.87        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        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-A29T TCGA-EE-A29W TCGA-EE-A29X 
       66.74        14.47        61.28       369.93       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       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-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       64.04        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        35.44        13.94         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       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        49.48         8.88       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 
       55.59        13.51        19.30         9.90        19.43        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  CDK4 MUTATED CDK4 WILD-TYPE 
          2.04           0.20 
  CDK4 MUTATED CDK4 WILD-TYPE 
        148.18         369.93 
  CDK4 MUTATED CDK4 WILD-TYPE 
        27.320         54.215 
[1] "2.0 - 148.2 (27.3)" "0.2 - 369.9 (54.2)"
[1] "hr=" "2"  
D16V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CDK4 MUTATED          0       0       1        0        1        0         0
  CDK4 WILD-TYPE       10       6      24       10       24       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CDK4 MUTATED           1         0         1          1          1          1
  CDK4 WILD-TYPE        13        10        35         13         25         42
                vv
clus             STAGE IV
  CDK4 MUTATED          0
  CDK4 WILD-TYPE       16
D16V4, multiclass
            clus
vv           CDK4 MUTATED CDK4 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               1             24
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             1             13
  STAGE IIC             0             10
  STAGE III             1             35
  STAGE IIIA            1             13
  STAGE IIIB            1             25
  STAGE IIIC            1             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
  CDK4 MUTATED       1  3  2  0
  CDK4 WILD-TYPE    52 59 58 55
D16V5, multiclass
       clus
vv      CDK4 MUTATED CDK4 WILD-TYPE
  T0+T1            1             52
  T2               3             59
  T3               2             58
  T4               0             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CDK4 MUTATED     2   3   1   0
  CDK4 WILD-TYPE 141  50  33  35
D16V6, multiclass
    clus
vv   CDK4 MUTATED CDK4 WILD-TYPE
  N0            2            141
  N1            3             50
  N2            1             33
  N3            0             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"
D16V7, binary
                cls
clus               0   1
  CDK4 MUTATED     7   0
  CDK4 WILD-TYPE 249  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      7    0
  CDK4 WILD-TYPE  249   17
   clus
vv  CDK4 MUTATED CDK4 WILD-TYPE
  0            7            249
  1            0             17
[1] 2 2
[1] FALSE
D16V8, binary
                cls
clus               0   1
  CDK4 MUTATED     3   2
  CDK4 WILD-TYPE 104  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      3    2
  CDK4 WILD-TYPE  104   71
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  NO             3            104
  YES            2             71
[1] 2 2
[1] FALSE
D16V9, binary
                cls
clus               0   1
  CDK4 MUTATED     1   7
  CDK4 WILD-TYPE  36 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      1    7
  CDK4 WILD-TYPE   36  246
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  NO             1             36
  YES            7            246
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, binary
                cls
clus               0   1
  CDK4 MUTATED     3   5
  CDK4 WILD-TYPE 106 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      3    5
  CDK4 WILD-TYPE  106  176
        clus
vv       CDK4 MUTATED CDK4 WILD-TYPE
  FEMALE            3            106
  MALE              5            176
[1] 2 2
[1] FALSE
D16V12, binary
                cls
clus               0   1
  CDK4 MUTATED     8   0
  CDK4 WILD-TYPE 246  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      8    0
  CDK4 WILD-TYPE  246   35
     clus
vv    CDK4 MUTATED CDK4 WILD-TYPE
  NO             8            246
  YES            0             35
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDK4 MUTATED       1                         0     7
  CDK4 WILD-TYPE     4                         1   277
D16V13, multiclass
                           clus
vv                          CDK4 MUTATED CDK4 WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                7            277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                cls
clus               0   1
  CDK4 MUTATED     0   8
  CDK4 WILD-TYPE   3 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDK4 MUTATED      0    8
  CDK4 WILD-TYPE    3  275
                        clus
vv                       CDK4 MUTATED CDK4 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            8            275
[1] 2 2
[1] FALSE

Clustering(17) Variable = DSG3 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  DSG3 MUTATED   14 20
  DSG3 WILD-TYPE 83 83
  DSG3 MUTATED DSG3 WILD-TYPE 
            34            166 
  DSG3 MUTATED DSG3 WILD-TYPE 
            20             83 
$`DSG3 MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JA 
      166.75        52.90       134.40        27.35        36.85        15.75 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC 
       76.34       138.67       150.61       110.53        60.10        58.85 
TCGA-EB-A44Q TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A2GJ 
        3.91        20.38         0.00        26.24         0.26        68.65 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ 
       93.63         0.20       103.13        23.77       171.85        63.25 
TCGA-EE-A3AF TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-FS-A1Z3 
        6.28       184.60        42.51       120.76        47.18         8.35 
TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-GN-A4U4 
      130.95         3.06        80.68        34.49 

$`DSG3 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-ER-A193 
       62.07        38.76        33.24        31.96       269.03        19.04 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 
      177.86        15.02        22.29        69.21        22.85        68.68 
TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN 
       64.83        30.44       225.11        42.64        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       18.21        13.15        24.89        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14        12.99        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       26.14        12.95       201.60        10.62        32.48        18.35 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF 
        0.76        71.31        81.99        15.25         5.75       209.79 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       94.19        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81        11.47       150.12        99.06        59.84 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       49.71       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV 
       18.51        66.67       173.19        13.28        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 
       96.92        17.06        42.48         7.59       120.53        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  DSG3 MUTATED DSG3 WILD-TYPE 
           0.0            0.2 
  DSG3 MUTATED DSG3 WILD-TYPE 
        184.60         346.49 
  DSG3 MUTATED DSG3 WILD-TYPE 
        55.875         46.455 
[1] "0.0 - 184.6 (55.9)" "0.2 - 346.5 (46.5)"
[1] "hr=" "1.3"
D17V2, survival
                sevent
clus2              0   1
  DSG3 MUTATED    19  28
  DSG3 WILD-TYPE 105 132
  DSG3 MUTATED DSG3 WILD-TYPE 
            47            237 
  DSG3 MUTATED DSG3 WILD-TYPE 
            28            132 
$`DSG3 MUTATED`
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 
      168.26         2.60       126.81       134.40        27.35        36.95 
TCGA-D3-A2JA TCGA-D3-A3C7 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
      115.53        46.98         9.90        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-EB-A44Q 
       20.38       176.55       135.02        88.87        68.09        13.87 
TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A29R 
       29.29        33.73        14.70        26.89        63.78        14.47 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 
       39.29        67.43       107.38       102.12        42.77       129.27 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-ER-A19G 
       61.51       204.66        96.23        13.81        36.95       302.07 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       44.09       162.08        49.48        20.91        23.93       133.55 
TCGA-FS-A1ZZ TCGA-FS-A4FC TCGA-FS-A4FD TCGA-GN-A266 TCGA-GN-A4U4 
       27.02        54.41        80.68        10.13        39.35 

$`DSG3 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A2GD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 
       68.15       340.14        31.40        50.76        15.45        16.57 
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-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-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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-A6EA 
       54.67         3.65         7.10        15.39        22.29        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA 
       77.56        22.95       222.51        35.93        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
       40.60        33.93        10.49       225.96        43.36        10.36 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
        8.65         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        66.74        61.28       369.93 
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       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       86.14        59.28       173.79       220.24        48.72        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       79.66        75.48        13.91        81.21        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      103.20        16.96       180.39       216.66       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        64.04        28.77        54.51        41.59       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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19T 
      152.35         6.44       131.51        61.05        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38       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-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
      174.84        34.03        26.73        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
      121.91        10.42        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  DSG3 MUTATED DSG3 WILD-TYPE 
           2.6            0.2 
  DSG3 MUTATED DSG3 WILD-TYPE 
        302.07         369.93 
  DSG3 MUTATED DSG3 WILD-TYPE 
         49.48          54.02 
[1] "2.6 - 302.1 (49.5)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.1"
D17V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DSG3 MUTATED          1       1       4        1        1        4         3
  DSG3 WILD-TYPE        9       5      21        9       24       14         7
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DSG3 MUTATED           3         0         8          2          5          6
  DSG3 WILD-TYPE        11        10        28         12         21         37
                vv
clus             STAGE IV
  DSG3 MUTATED          4
  DSG3 WILD-TYPE       12
D17V4, multiclass
            clus
vv           DSG3 MUTATED DSG3 WILD-TYPE
  I/II NOS              1              9
  STAGE 0               1              5
  STAGE I               4             21
  STAGE IA              1              9
  STAGE IB              1             24
  STAGE II              4             14
  STAGE IIA             3              7
  STAGE IIB             3             11
  STAGE IIC             0             10
  STAGE III             8             28
  STAGE IIIA            2             12
  STAGE IIIB            5             21
  STAGE IIIC            6             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
  DSG3 MUTATED       8  9  9  9
  DSG3 WILD-TYPE    45 53 51 46
D17V5, multiclass
       clus
vv      DSG3 MUTATED DSG3 WILD-TYPE
  T0+T1            8             45
  T2               9             53
  T3               9             51
  T4               9             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DSG3 MUTATED    22  10   6   5
  DSG3 WILD-TYPE 121  43  28  30
D17V6, multiclass
    clus
vv   DSG3 MUTATED DSG3 WILD-TYPE
  N0           22            121
  N1           10             43
  N2            6             28
  N3            5             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"
D17V7, binary
                cls
clus               0   1
  DSG3 MUTATED    41   4
  DSG3 WILD-TYPE 215  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     41    4
  DSG3 WILD-TYPE  215   13
   clus
vv  DSG3 MUTATED DSG3 WILD-TYPE
  0           41            215
  1            4             13
[1] 2 2
[1] FALSE
D17V8, binary
                cls
clus              0  1
  DSG3 MUTATED   16 11
  DSG3 WILD-TYPE 91 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     16   11
  DSG3 WILD-TYPE   91   62
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO            16             91
  YES           11             62
[1] 2 2
[1] FALSE
D17V9, binary
                cls
clus               0   1
  DSG3 MUTATED     9  39
  DSG3 WILD-TYPE  28 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      9   39
  DSG3 WILD-TYPE   28  214
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO             9             28
  YES           39            214
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, binary
                cls
clus               0   1
  DSG3 MUTATED    17  31
  DSG3 WILD-TYPE  92 150
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     17   31
  DSG3 WILD-TYPE   92  150
        clus
vv       DSG3 MUTATED DSG3 WILD-TYPE
  FEMALE           17             92
  MALE             31            150
[1] 2 2
[1] FALSE
D17V12, binary
                cls
clus               0   1
  DSG3 MUTATED    42   6
  DSG3 WILD-TYPE 212  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     42    6
  DSG3 WILD-TYPE  212   29
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO            42            212
  YES            6             29
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSG3 MUTATED       1                         0    47
  DSG3 WILD-TYPE     4                         1   237
D17V13, multiclass
                           clus
vv                          DSG3 MUTATED DSG3 WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               47            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"
D17V14, binary
                cls
clus               0   1
  DSG3 MUTATED     1  47
  DSG3 WILD-TYPE   2 236
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      1   47
  DSG3 WILD-TYPE    2  236
                        clus
vv                       DSG3 MUTATED DSG3 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           47            236
[1] 2 2
[1] FALSE

Clustering(18) Variable = MLL MUTATION ANALYSIS
D18V1, survival
               sevent
clus2            0  1
  MLL MUTATED   14 15
  MLL WILD-TYPE 83 88
  MLL MUTATED MLL WILD-TYPE 
           29           171 
  MLL MUTATED MLL WILD-TYPE 
           15            88 
$`MLL MUTATED`
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A51T TCGA-D9-A3Z1 TCGA-DA-A1HY 
      134.40        19.04        36.85        11.34        15.02       138.67 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A2A2 TCGA-EE-A2GN 
      110.53        60.10        42.64        20.38        30.02        93.63 
TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A19A 
      124.31         6.28       111.85        45.90         3.35         4.54 
TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZC 
       47.18        22.36        68.52       171.78         8.35       312.07 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3TU TCGA-OD-A75X 
      136.27        23.21         3.06        55.59       297.01 

$`MLL WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.90        27.35         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       42.05        45.70       177.86        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       76.34        68.68       150.61        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
      225.11         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       24.89         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       27.16        61.12       346.49       185.19       115.43        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       122.73        64.04         4.41        54.51 
TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       67.89       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       99.06        59.84        42.51       120.76        49.71       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YY 
       15.48        32.05        74.47         4.50       174.21        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      195.98        27.62        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
       78.61       130.95        35.28         4.47         5.29        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67       173.19        13.28        80.68        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  MLL MUTATED MLL WILD-TYPE 
         3.06          0.00 
  MLL MUTATED MLL WILD-TYPE 
       312.07        346.49 
  MLL MUTATED MLL WILD-TYPE 
        45.90         47.74 
[1] "3.1 - 312.1 (45.9)" "0.0 - 346.5 (47.7)"
[1] "hr=" "1.1"
D18V2, survival
               sevent
clus2             0   1
  MLL MUTATED    18  21
  MLL WILD-TYPE 106 139
  MLL MUTATED MLL WILD-TYPE 
           39           245 
  MLL MUTATED MLL WILD-TYPE 
           21           139 
$`MLL MUTATED`
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A3C7 TCGA-D3-A51T TCGA-D9-A3Z1 
      134.40        31.40        36.95        46.98        26.89        15.39 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A181 
      144.89        20.38       135.02        88.87        43.36        33.73 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A3AA 
       25.87        59.64        67.43        48.72       102.12       124.31 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       13.81       127.20        36.95        64.08        34.32        53.19 
TCGA-ER-A19A TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1Z3 
       77.75        49.48        43.82        93.01       216.92        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3TU 
       27.72       357.37       148.80        49.48        27.02        55.59 
TCGA-GF-A6C9 TCGA-GN-A26D TCGA-OD-A75X 
       15.78        48.00       297.90 

$`MLL WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       126.81        27.35 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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-A3CB 
       66.48        66.08        59.57       130.72        58.06       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81       125.79       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         7.10 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA 
       36.03       222.51       176.55        35.93        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       40.60        68.09        33.93        10.49       225.96        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       78.97        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-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      195.02        17.92        46.82       115.96        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       59.28       173.79       220.24       107.38        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        42.77        81.21        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 
      180.39       216.66       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        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JE 
       54.51        41.59       138.81       172.18       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      134.33       152.81        35.44        13.94         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       302.07       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        44.09       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       105.07        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       48.99        41.56       247.04        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1YY 
      149.03        92.98       174.21        15.72        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
      202.65        28.08         7.79        48.85        53.52        46.45 
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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        17.46        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       62.79        32.48       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13         7.23         0.20         0.33         0.69 

  MLL MUTATED MLL WILD-TYPE 
        13.81          0.20 
  MLL MUTATED MLL WILD-TYPE 
       357.37        369.93 
  MLL MUTATED MLL WILD-TYPE 
        49.48         54.51 
[1] "13.8 - 357.4 (49.5)" "0.2 - 369.9 (54.5)" 
[1] "hr=" "1.1"
D18V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MLL MUTATED          2       0       3        1        3        2         1
  MLL WILD-TYPE        8       6      22        9       22       16         9
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MLL MUTATED           3         1         5          2          5          5
  MLL WILD-TYPE        11         9        31         12         21         38
               vv
clus            STAGE IV
  MLL MUTATED          4
  MLL WILD-TYPE       12
D18V4, multiclass
            clus
vv           MLL MUTATED MLL WILD-TYPE
  I/II NOS             2             8
  STAGE 0              0             6
  STAGE I              3            22
  STAGE IA             1             9
  STAGE IB             3            22
  STAGE II             2            16
  STAGE IIA            1             9
  STAGE IIB            3            11
  STAGE IIC            1             9
  STAGE III            5            31
  STAGE IIIA           2            12
  STAGE IIIB           5            21
  STAGE IIIC           5            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
  MLL MUTATED       7 10  7  7
  MLL WILD-TYPE    46 52 53 48
D18V5, multiclass
       clus
vv      MLL MUTATED MLL WILD-TYPE
  T0+T1           7            46
  T2             10            52
  T3              7            53
  T4              7            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  MLL MUTATED    19   9   5   3
  MLL WILD-TYPE 124  44  29  32
D18V6, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  N0          19           124
  N1           9            44
  N2           5            29
  N3           3            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"
D18V7, binary
               cls
clus              0   1
  MLL MUTATED    32   4
  MLL WILD-TYPE 224  13
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     32    4
  MLL WILD-TYPE  224   13
   clus
vv  MLL MUTATED MLL WILD-TYPE
  0          32           224
  1           4            13
[1] 2 2
[1] FALSE
D18V8, binary
               cls
clus             0  1
  MLL MUTATED   10 13
  MLL WILD-TYPE 97 60
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     10   13
  MLL WILD-TYPE   97   60
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO           10            97
  YES          13            60
[1] 2 2
[1] FALSE
D18V9, binary
               cls
clus              0   1
  MLL MUTATED     8  32
  MLL WILD-TYPE  29 221
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      8   32
  MLL WILD-TYPE   29  221
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO            8            29
  YES          32           221
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, binary
               cls
clus              0   1
  MLL MUTATED    13  27
  MLL WILD-TYPE  96 154
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     13   27
  MLL WILD-TYPE   96  154
        clus
vv       MLL MUTATED MLL WILD-TYPE
  FEMALE          13            96
  MALE            27           154
[1] 2 2
[1] FALSE
D18V12, binary
               cls
clus              0   1
  MLL MUTATED    34   6
  MLL WILD-TYPE 220  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED     34    6
  MLL WILD-TYPE  220   29
     clus
vv    MLL MUTATED MLL WILD-TYPE
  NO           34           220
  YES           6            29
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL MUTATED       0                         0    40
  MLL WILD-TYPE     5                         1   244
D18V13, multiclass
                           clus
vv                          MLL MUTATED MLL WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              40           244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
               cls
clus              0   1
  MLL MUTATED     1  39
  MLL WILD-TYPE   2 244
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      1   39
  MLL WILD-TYPE    2  244
                        clus
vv                       MLL MUTATED MLL WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          39           244
[1] 2 2
[1] FALSE

Clustering(19) Variable = DDX3X MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2              0  1
  DDX3X MUTATED    6  8
  DDX3X WILD-TYPE 91 95
  DDX3X MUTATED DDX3X WILD-TYPE 
             14             186 
  DDX3X MUTATED DDX3X WILD-TYPE 
              8              95 
$`DDX3X MUTATED`
TCGA-ER-A193 TCGA-D3-A2J8 TCGA-DA-A3F8 TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GN 
       19.04        62.86        42.64         0.26       115.43        93.63 
TCGA-EE-A2GP TCGA-EE-A2ML TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J7 
        0.76       104.78        53.26       124.31         6.28        45.90 
TCGA-FS-A1Z3 TCGA-OD-A75X 
        8.35       297.01 

$`DDX3X WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        27.35        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       62.60        25.64        45.99        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
      225.11         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14        12.99        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 
       27.16        61.12       346.49       185.19        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       18.35         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
       89.26       145.45       227.01       143.93        23.51       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       64.04         4.41        54.51        67.89       111.85         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.50       174.21       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      120.53        34.49        46.92         7.23         0.20         0.33 

  DDX3X MUTATED DDX3X WILD-TYPE 
           0.26            0.00 
  DDX3X MUTATED DDX3X WILD-TYPE 
         297.01          346.49 
  DDX3X MUTATED DDX3X WILD-TYPE 
         49.580          47.295 
[1] "0.3 - 297.0 (49.6)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.1"
D19V2, survival
                 sevent
clus2               0   1
  DDX3X MUTATED    10  10
  DDX3X WILD-TYPE 114 150
  DDX3X MUTATED DDX3X WILD-TYPE 
             20             264 
  DDX3X MUTATED DDX3X WILD-TYPE 
             10             150 
$`DDX3X MUTATED`
TCGA-ER-A193 TCGA-D3-A2J8 TCGA-D9-A148 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A3F8 
       31.40        65.49       151.53        25.18        20.38        43.36 
TCGA-EE-A20B TCGA-EE-A29E TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GN TCGA-EE-A2GP 
      133.81        63.78       115.96        67.43       102.12        13.91 
TCGA-EE-A2ML TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-FS-A1Z3 
      216.66        53.26       124.31        13.81        64.08        20.91 
TCGA-FS-A1ZK TCGA-OD-A75X 
       23.93       297.90 

$`DDX3X WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       27.35        50.76        15.45        36.95        16.57        16.67 
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-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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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-A6EC 
        3.65         7.10        15.39        22.29         9.90        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03       144.89       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        33.93        10.49       225.96        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
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        85.08        78.97 
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-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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        59.64        39.29        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       75.48        42.77        81.21        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       180.39 
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-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        64.04        28.77        54.51        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18       127.20        36.95        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       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        46.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13         7.23         0.20         0.33         0.69 

  DDX3X MUTATED DDX3X WILD-TYPE 
          13.81            0.20 
  DDX3X MUTATED DDX3X WILD-TYPE 
         297.90          369.93 
  DDX3X MUTATED DDX3X WILD-TYPE 
          63.93           53.72 
[1] "13.8 - 297.9 (63.9)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1.3"
D19V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DDX3X MUTATED          0       0       1        1        2        3         1
  DDX3X WILD-TYPE       10       6      24        9       23       15         9
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DDX3X MUTATED           2         0         1          0          3
  DDX3X WILD-TYPE        12        10        35         14         23
                 vv
clus              STAGE IIIC STAGE IV
  DDX3X MUTATED            2        2
  DDX3X WILD-TYPE         41       14
D19V4, multiclass
            clus
vv           DDX3X MUTATED DDX3X WILD-TYPE
  I/II NOS               0              10
  STAGE 0                0               6
  STAGE I                1              24
  STAGE IA               1               9
  STAGE IB               2              23
  STAGE II               3              15
  STAGE IIA              1               9
  STAGE IIB              2              12
  STAGE IIC              0              10
  STAGE III              1              35
  STAGE IIIA             0              14
  STAGE IIIB             3              23
  STAGE IIIC             2              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
  DDX3X MUTATED       3  5  5  4
  DDX3X WILD-TYPE    50 57 55 51
D19V5, multiclass
       clus
vv      DDX3X MUTATED DDX3X WILD-TYPE
  T0+T1             3              50
  T2                5              57
  T3                5              55
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDX3X MUTATED    11   2   2   4
  DDX3X WILD-TYPE 132  51  32  31
D19V6, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  N0            11             132
  N1             2              51
  N2             2              32
  N3             4              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"
D19V7, binary
                 cls
clus                0   1
  DDX3X MUTATED    17   3
  DDX3X WILD-TYPE 239  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED     17    3
  DDX3X WILD-TYPE  239   14
   clus
vv  DDX3X MUTATED DDX3X WILD-TYPE
  0            17             239
  1             3              14
[1] 2 2
[1] FALSE
D19V8, binary
                 cls
clus               0  1
  DDX3X MUTATED    9  5
  DDX3X WILD-TYPE 98 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      9    5
  DDX3X WILD-TYPE   98   68
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              9              98
  YES             5              68
[1] 2 2
[1] FALSE
D19V9, binary
                 cls
clus                0   1
  DDX3X MUTATED     3  17
  DDX3X WILD-TYPE  34 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      3   17
  DDX3X WILD-TYPE   34  236
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              3              34
  YES            17             236
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, binary
                 cls
clus                0   1
  DDX3X MUTATED     3  17
  DDX3X WILD-TYPE 106 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      3   17
  DDX3X WILD-TYPE  106  164
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  FEMALE             3             106
  MALE              17             164
[1] 2 2
[1] FALSE
D19V12, binary
                 cls
clus                0   1
  DDX3X MUTATED    18   2
  DDX3X WILD-TYPE 236  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED     18    2
  DDX3X WILD-TYPE  236   33
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO             18             236
  YES             2              33
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX3X MUTATED       0                         0    20
  DDX3X WILD-TYPE     5                         1   264
D19V13, multiclass
                           clus
vv                          DDX3X MUTATED DDX3X WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                20             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"
D19V14, binary
                 cls
clus                0   1
  DDX3X MUTATED     0  20
  DDX3X WILD-TYPE   3 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      0   20
  DDX3X WILD-TYPE    3  263
                        clus
vv                       DDX3X MUTATED DDX3X WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            20             263
[1] 2 2
[1] FALSE

Clustering(20) Variable = HSD11B1 MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                 0   1
  HSD11B1 MUTATED     9   1
  HSD11B1 WILD-TYPE  88 102
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               10               190 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                1               102 
$`HSD11B1 MUTATED`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A2JH 
       62.07        33.24       134.40        36.85        49.35        36.30 
TCGA-D3-A51T TCGA-EE-A29M TCGA-EE-A2GM TCGA-QB-A6FS 
       11.34        47.74        18.35         7.23 

$`HSD11B1 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       38.76        31.96       166.75       269.03        52.90        27.35 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       19.04         8.42        15.72        31.89       110.93       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN 
       15.75       168.00        86.30       107.61       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        31.76        62.70        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         0.20         0.33 

  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
             7.23              0.00 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           134.40            346.49 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           36.575            48.560 
[1] "7.2 - 134.4 (36.6)" "0.0 - 346.5 (48.6)"
[1] "hr=" "3.4"
D20V2, survival
                   sevent
clus2                 0   1
  HSD11B1 MUTATED    10   4
  HSD11B1 WILD-TYPE 114 156
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
               14               270 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
                4               156 
$`HSD11B1 MUTATED`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A2JH 
       62.07        68.25       134.40        36.95        71.80        42.08 
TCGA-D3-A51T TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2MD 
       26.89        56.84        14.47        46.82        75.48        47.28 
TCGA-EE-A2MQ TCGA-QB-A6FS 
       43.23         7.23 

$`HSD11B1 WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       46.32        13.87        54.02        94.98        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
        2.60       340.14       126.81        27.35        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       15.45        16.57        16.67       112.04       112.57       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-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        12.10       171.58        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       13.97        63.78        72.07        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       66.74        61.28       369.93        25.87       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      216.66       167.90        47.54       248.65       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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13       297.90         0.20         0.33         0.69 

  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
             7.23              0.20 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           134.40            369.93 
  HSD11B1 MUTATED HSD11B1 WILD-TYPE 
           47.050            54.215 
[1] "7.2 - 134.4 (47.0)" "0.2 - 369.9 (54.2)"
[1] "hr=" "1.5"
D20V3, continuous
                   vv
clus                I/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      24        9       23       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  HSD11B1 MUTATED           1         0         1         2          1
  HSD11B1 WILD-TYPE         9        14         9        34         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  HSD11B1 MUTATED            0          3        0
  HSD11B1 WILD-TYPE         26         40       16
D20V4, multiclass
            clus
vv           HSD11B1 MUTATED HSD11B1 WILD-TYPE
  I/II NOS                 0                10
  STAGE 0                  0                 6
  STAGE I                  1                24
  STAGE IA                 1                 9
  STAGE IB                 2                23
  STAGE II                 1                17
  STAGE IIA                1                 9
  STAGE IIB                0                14
  STAGE IIC                1                 9
  STAGE III                2                34
  STAGE IIIA               1                13
  STAGE IIIB               0                26
  STAGE IIIC               3                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
  HSD11B1 MUTATED       3  2  4  3
  HSD11B1 WILD-TYPE    50 60 56 52
D20V5, multiclass
       clus
vv      HSD11B1 MUTATED HSD11B1 WILD-TYPE
  T0+T1               3                50
  T2                  2                60
  T3                  4                56
  T4                  3                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HSD11B1 MUTATED     7   3   2   1
  HSD11B1 WILD-TYPE 136  50  32  34
D20V6, multiclass
    clus
vv   HSD11B1 MUTATED HSD11B1 WILD-TYPE
  N0               7               136
  N1               3                50
  N2               2                32
  N3               1                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"
D20V7, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED    13   0
  HSD11B1 WILD-TYPE 243  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED     13    0
  HSD11B1 WILD-TYPE  243   17
   clus
vv  HSD11B1 MUTATED HSD11B1 WILD-TYPE
  0              13               243
  1               0                17
[1] 2 2
[1] FALSE
D20V8, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     7   4
  HSD11B1 WILD-TYPE 100  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      7    4
  HSD11B1 WILD-TYPE  100   69
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO                7               100
  YES               4                69
[1] 2 2
[1] FALSE
D20V9, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     1  13
  HSD11B1 WILD-TYPE  36 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      1   13
  HSD11B1 WILD-TYPE   36  240
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO                1                36
  YES              13               240
[1] 2 2
[1] FALSE
D20V10, continuous
D20V11, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED     7   7
  HSD11B1 WILD-TYPE 102 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      7    7
  HSD11B1 WILD-TYPE  102  174
        clus
vv       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  FEMALE               7               102
  MALE                 7               174
[1] 2 2
[1] FALSE
D20V12, binary
                   cls
clus                  0   1
  HSD11B1 MUTATED    11   3
  HSD11B1 WILD-TYPE 243  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED     11    3
  HSD11B1 WILD-TYPE  243   32
     clus
vv    HSD11B1 MUTATED HSD11B1 WILD-TYPE
  NO               11               243
  YES               3                32
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSD11B1 MUTATED       0                         0    14
  HSD11B1 WILD-TYPE     5                         1   270
D20V13, multiclass
                           clus
vv                          HSD11B1 MUTATED HSD11B1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  14               270
[1] 3 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
  HSD11B1 MUTATED     0  14
  HSD11B1 WILD-TYPE   3 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD11B1 MUTATED      0   14
  HSD11B1 WILD-TYPE    3  269
                        clus
vv                       HSD11B1 MUTATED HSD11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              14               269
[1] 2 2
[1] FALSE

Clustering(21) Variable = ALPK2 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2              0  1
  ALPK2 MUTATED   13 14
  ALPK2 WILD-TYPE 84 89
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             27             173 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             14              89 
$`ALPK2 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JG TCGA-D3-A2JO 
       52.90       134.40        27.35        36.85       107.61        66.08 
TCGA-D3-A3MR TCGA-D3-A51R TCGA-D9-A6EC TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 
       90.21        62.70        69.21        58.85        24.89        20.38 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P 
       26.24        75.55        79.20        12.99         0.26        27.16 
TCGA-EE-A2GJ TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AC TCGA-ER-A19A TCGA-ER-A19N 
       68.65        63.25        53.26        64.04         4.54        42.51 
TCGA-ER-A19P TCGA-ER-A2NE TCGA-FS-A1Z3 
      120.76        16.87         8.35 

$`ALPK2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86        15.75       168.00        86.30        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       31.76        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.29        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        60.10        64.83        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
        3.91        16.41        52.41        18.21        13.15         0.00 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       75.22        76.14        44.28        47.41        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95       201.60        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
        5.75        23.77       209.79        94.19       171.85        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      104.78       145.45       227.01       143.93        23.51       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       10.49         7.82        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      150.12        99.06        59.84        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05        22.36         4.70        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      171.78        49.74       195.98        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           0.26            0.00 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
         134.40          346.49 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          53.26           46.92 
[1] "0.3 - 134.4 (53.3)" "0.0 - 346.5 (46.9)"
[1] "hr=" "1.4"
D21V2, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    19  26
  ALPK2 WILD-TYPE 105 134
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             45             239 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             26             134 
$`ALPK2 MUTATED`
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FS-A1ZF TCGA-FW-A3R5 
        2.60       126.81       134.40        27.35        15.45        36.95 
TCGA-D3-A2JG TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A5GO 
      113.52        66.08       103.59        45.30        63.81       137.92 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 
       25.18        77.56        68.09        27.22        33.73        26.89 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29S 
      151.27        91.56        13.97        63.78        56.42        61.28 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ 
       39.29        67.43       107.38        21.67        47.28        96.23 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-ER-A19A TCGA-ER-A19N 
       53.26        64.04        41.59        36.95        77.75        44.09 
TCGA-ER-A19P TCGA-ER-A2NE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZP 
      162.08        20.15        20.91        27.72        48.85        74.73 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-RP-A694 
       15.78        10.13         0.69 

$`ALPK2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-ER-A193 TCGA-ER-A198 TCGA-D3-A1Q1 
       68.15       168.26       340.14        31.40        50.76        16.57 
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-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-A2JH 
       23.77       115.53       168.00        86.76        11.87        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10       171.58        66.48        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         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-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       22.29         9.90        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       53.92        65.92        40.60        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 
        7.04        36.46        29.82         8.65        14.70         4.96 
TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
      133.81        13.55        63.35        85.08        78.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
       64.64        56.84        18.61        66.74        14.47       369.93 
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       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       86.14        59.28       173.79       220.24        48.72        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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-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       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      216.66       167.90        47.54       248.65        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       71.21       124.31       122.73        28.77        54.51        13.81 
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-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q 
      302.07       152.35         6.44       131.51        61.05        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       22.13       297.90         7.23         0.20         0.33 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           0.69            0.20 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
         162.08          369.93 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          48.85           54.41 
[1] "0.7 - 162.1 (48.9)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.3"
D21V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ALPK2 MUTATED          1       4       3        2        1        6         2
  ALPK2 WILD-TYPE        9       2      22        8       24       12         8
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ALPK2 MUTATED           1         2         7          2          6
  ALPK2 WILD-TYPE        13         8        29         12         20
                 vv
clus              STAGE IIIC STAGE IV
  ALPK2 MUTATED            4        3
  ALPK2 WILD-TYPE         39       13
D21V4, multiclass
            clus
vv           ALPK2 MUTATED ALPK2 WILD-TYPE
  I/II NOS               1               9
  STAGE 0                4               2
  STAGE I                3              22
  STAGE IA               2               8
  STAGE IB               1              24
  STAGE II               6              12
  STAGE IIA              2               8
  STAGE IIB              1              13
  STAGE IIC              2               8
  STAGE III              7              29
  STAGE IIIA             2              12
  STAGE IIIB             6              20
  STAGE IIIC             4              39
  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
  ALPK2 MUTATED       6  5 14  8
  ALPK2 WILD-TYPE    47 57 46 47
D21V5, multiclass
       clus
vv      ALPK2 MUTATED ALPK2 WILD-TYPE
  T0+T1             6              47
  T2                5              57
  T3               14              46
  T4                8              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ALPK2 MUTATED    26   7   7   3
  ALPK2 WILD-TYPE 117  46  27  32
D21V6, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  N0            26             117
  N1             7              46
  N2             7              27
  N3             3              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"
D21V7, binary
                 cls
clus                0   1
  ALPK2 MUTATED    41   3
  ALPK2 WILD-TYPE 215  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     41    3
  ALPK2 WILD-TYPE  215   14
   clus
vv  ALPK2 MUTATED ALPK2 WILD-TYPE
  0            41             215
  1             3              14
[1] 2 2
[1] FALSE
D21V8, binary
                 cls
clus               0  1
  ALPK2 MUTATED   16 10
  ALPK2 WILD-TYPE 91 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     16   10
  ALPK2 WILD-TYPE   91   63
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             16              91
  YES            10              63
[1] 2 2
[1] FALSE
D21V9, binary
                 cls
clus                0   1
  ALPK2 MUTATED    10  37
  ALPK2 WILD-TYPE  27 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     10   37
  ALPK2 WILD-TYPE   27  216
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             10              27
  YES            37             216
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, binary
                 cls
clus                0   1
  ALPK2 MUTATED    11  36
  ALPK2 WILD-TYPE  98 145
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     11   36
  ALPK2 WILD-TYPE   98  145
        clus
vv       ALPK2 MUTATED ALPK2 WILD-TYPE
  FEMALE            11              98
  MALE              36             145
[1] 2 2
[1] FALSE
D21V12, binary
                 cls
clus                0   1
  ALPK2 MUTATED    40   7
  ALPK2 WILD-TYPE 214  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     40    7
  ALPK2 WILD-TYPE  214   28
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             40             214
  YES             7              28
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALPK2 MUTATED       1                         0    46
  ALPK2 WILD-TYPE     4                         1   238
D21V13, multiclass
                           clus
vv                          ALPK2 MUTATED ALPK2 WILD-TYPE
  ASIAN                                 1               4
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                46             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"
D21V14, binary
                 cls
clus                0   1
  ALPK2 MUTATED     0  46
  ALPK2 WILD-TYPE   3 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED      0   46
  ALPK2 WILD-TYPE    3  237
                        clus
vv                       ALPK2 MUTATED ALPK2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            46             237
[1] 2 2
[1] FALSE

Clustering(22) Variable = ATP5F1 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  ATP5F1 MUTATED     2   0
  ATP5F1 WILD-TYPE  95 103
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               2              198 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               0              103 
$`ATP5F1 MUTATED`
TCGA-FW-A3R5 TCGA-EE-A3AE 
       36.85        54.51 

$`ATP5F1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        27.35        19.04         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        64.04         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           36.85             0.00 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           54.51           346.49 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
          45.680           47.295 
[1] "36.9 - 54.5 (45.7)" "0.0 - 346.5 (47.3)"
[1] "Remove cluster labels:" "ATP5F1 MUTATED"        
D22V2, survival
                  sevent
clus2                0   1
  ATP5F1 MUTATED     4   2
  ATP5F1 WILD-TYPE 120 158
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               6              278 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
               2              158 
$`ATP5F1 MUTATED`
TCGA-EE-A29L TCGA-FW-A3R5 TCGA-EE-A2GI TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A3AE 
        2.60        36.95        48.72        44.88        21.67        54.51 

$`ATP5F1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        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       173.79       220.24       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        13.81        41.59       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-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         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        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
             2.6              0.2 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
           54.51           369.93 
  ATP5F1 MUTATED ATP5F1 WILD-TYPE 
          40.915           54.540 
[1] "2.6 - 54.5 (40.9)"  "0.2 - 369.9 (54.5)"
[1] "hr=" "1.1"
D22V3, continuous
                  vv
clus               I/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      24        8       25       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ATP5F1 MUTATED           1         0         0         1          0
  ATP5F1 WILD-TYPE         9        14        10        35         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ATP5F1 MUTATED            0          1        0
  ATP5F1 WILD-TYPE         26         42       16
D22V4, multiclass
            clus
vv           ATP5F1 MUTATED ATP5F1 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                2                8
  STAGE IB                0               25
  STAGE II                0               18
  STAGE IIA               1                9
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               1               35
  STAGE IIIA              0               14
  STAGE IIIB              0               26
  STAGE IIIC              1               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
  ATP5F1 MUTATED       2  1  1  1
  ATP5F1 WILD-TYPE    51 61 59 54
D22V5, multiclass
       clus
vv      ATP5F1 MUTATED ATP5F1 WILD-TYPE
  T0+T1              2               51
  T2                 1               61
  T3                 1               59
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ATP5F1 MUTATED     4   0   1   1
  ATP5F1 WILD-TYPE 139  53  33  34
D22V6, multiclass
    clus
vv   ATP5F1 MUTATED ATP5F1 WILD-TYPE
  N0              4              139
  N1              0               53
  N2              1               33
  N3              1               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"
D22V7, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     6   0
  ATP5F1 WILD-TYPE 250  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      6    0
  ATP5F1 WILD-TYPE  250   17
   clus
vv  ATP5F1 MUTATED ATP5F1 WILD-TYPE
  0              6              250
  1              0               17
[1] 2 2
[1] FALSE
D22V8, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     4   1
  ATP5F1 WILD-TYPE 103  72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      4    1
  ATP5F1 WILD-TYPE  103   72
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  NO               4              103
  YES              1               72
[1] 2 2
[1] FALSE
D22V9, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     0   6
  ATP5F1 WILD-TYPE  37 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      0    6
  ATP5F1 WILD-TYPE   37  247
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  NO               0               37
  YES              6              247
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     1   5
  ATP5F1 WILD-TYPE 108 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      1    5
  ATP5F1 WILD-TYPE  108  176
        clus
vv       ATP5F1 MUTATED ATP5F1 WILD-TYPE
  FEMALE              1              108
  MALE                5              176
[1] 2 2
[1] FALSE
D22V12, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     6   0
  ATP5F1 WILD-TYPE 248  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      6    0
  ATP5F1 WILD-TYPE  248   35
     clus
vv    ATP5F1 MUTATED ATP5F1 WILD-TYPE
  NO               6              248
  YES              0               35
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP5F1 MUTATED       0                         0     6
  ATP5F1 WILD-TYPE     5                         1   278
D22V13, multiclass
                           clus
vv                          ATP5F1 MUTATED ATP5F1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  6              278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                  cls
clus                 0   1
  ATP5F1 MUTATED     0   6
  ATP5F1 WILD-TYPE   3 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5F1 MUTATED      0    6
  ATP5F1 WILD-TYPE    3  277
                        clus
vv                       ATP5F1 MUTATED ATP5F1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              6              277
[1] 2 2
[1] FALSE

Clustering(23) Variable = RPTN MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  RPTN MUTATED   14 14
  RPTN WILD-TYPE 83 89
  RPTN MUTATED RPTN WILD-TYPE 
            28            172 
  RPTN MUTATED RPTN WILD-TYPE 
            14             89 
$`RPTN MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-D3-A2JN 
       62.07       269.03        19.04        36.85       110.93        64.83 
TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A17X 
       90.21       144.46        11.34        69.21        76.34        13.15 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GJ 
       20.38        75.55         0.26        47.74        77.98        68.65 
TCGA-EE-A2MJ TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3JB TCGA-ER-A19A TCGA-ER-A19P 
       63.25        54.51         6.28       168.85         4.54       120.76 
TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-GN-A4U4 
       22.36         8.35       312.07        34.49 

$`RPTN WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR 
       38.76        33.24        31.96       166.75        52.90       134.40 
TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       27.35         8.42        15.72        31.89        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K 
       24.53         9.34        23.67       173.85        30.67        31.76 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       62.70        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       16.41        52.41        18.21        24.89         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14        12.99        44.28        47.41 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       26.14        12.95       201.60        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J3 
       53.26       124.31       122.73        64.04         4.41        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      111.85        45.90         3.35        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       10.49         7.82        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        59.84        42.51        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZD 
      174.21       171.78        49.74       195.98        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 
       96.92        17.06        42.48         7.59       120.53        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  RPTN MUTATED RPTN WILD-TYPE 
          0.26           0.00 
  RPTN MUTATED RPTN WILD-TYPE 
        312.07         346.49 
  RPTN MUTATED RPTN WILD-TYPE 
        62.660         45.945 
[1] "0.3 - 312.1 (62.7)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1.2"
D23V2, survival
                sevent
clus2              0   1
  RPTN MUTATED    18  23
  RPTN WILD-TYPE 106 137
  RPTN MUTATED RPTN WILD-TYPE 
            41            243 
  RPTN MUTATED RPTN WILD-TYPE 
            23            137 
$`RPTN MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EE-A2GD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q5 
       62.07        13.87       340.14        31.40        36.95       112.57 
TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO 
       66.48        46.98       103.59       145.12        26.89       137.92 
TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A20C 
        3.65        77.56        76.57        29.82        33.73       151.27 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2M5 
       63.78        56.84        61.28        86.14       107.38        21.67 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JB 
       47.28        96.23        54.51        13.81        36.95       201.80 
TCGA-ER-A19A TCGA-ER-A19P TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A4F5 
       77.75       162.08        43.82        20.91       357.37        28.73 
TCGA-FS-A4FC TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U4 TCGA-GN-A4U7 
       54.41        15.78        10.13        39.35        10.42 

$`RPTN WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       46.32        68.25        54.02        94.98        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF 
        2.60       126.81       134.40        27.35        50.76        15.45 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
       39.75        45.30       174.84        55.73        56.35        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.62        63.81       125.79       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19       151.53        54.67         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        22.95        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        7.04        36.46        27.22         8.65        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       133.81        91.56        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       78.97        13.97        72.07        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       66.74        14.47       369.93        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       115.96        59.64        39.29        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24        48.72        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       180.39       216.66       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-A3AG TCGA-EE-A3AH 
      124.31       122.73        64.04        28.77        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      172.18       127.20        64.08        34.32        53.19        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      134.33       152.81        35.44        13.94         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       302.07       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        44.09        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18       105.07        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85        53.52        46.45         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-A4FD TCGA-FW-A3I3 
       66.67       174.84        34.03        26.73        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       48.00       121.91        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  RPTN MUTATED RPTN WILD-TYPE 
          3.65           0.20 
  RPTN MUTATED RPTN WILD-TYPE 
        357.37         369.93 
  RPTN MUTATED RPTN WILD-TYPE 
         54.51          53.52 
[1] "3.6 - 357.4 (54.5)" "0.2 - 369.9 (53.5)"
[1] "hr=" "1.1"
D23V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  RPTN MUTATED          2       1       1        5        3        3         3
  RPTN WILD-TYPE        8       5      24        5       22       15         7
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RPTN MUTATED           2         0         8          2          3          3
  RPTN WILD-TYPE        12        10        28         12         23         40
                vv
clus             STAGE IV
  RPTN MUTATED          3
  RPTN WILD-TYPE       13
D23V4, multiclass
            clus
vv           RPTN MUTATED RPTN WILD-TYPE
  I/II NOS              2              8
  STAGE 0               1              5
  STAGE I               1             24
  STAGE IA              5              5
  STAGE IB              3             22
  STAGE II              3             15
  STAGE IIA             3              7
  STAGE IIB             2             12
  STAGE IIC             0             10
  STAGE III             8             28
  STAGE IIIA            2             12
  STAGE IIIB            3             23
  STAGE IIIC            3             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
  RPTN MUTATED      12  6  9  5
  RPTN WILD-TYPE    41 56 51 50
D23V5, multiclass
       clus
vv      RPTN MUTATED RPTN WILD-TYPE
  T0+T1           12             41
  T2               6             56
  T3               9             51
  T4               5             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RPTN MUTATED    23   9   4   2
  RPTN WILD-TYPE 120  44  30  33
D23V6, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  N0           23            120
  N1            9             44
  N2            4             30
  N3            2             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"
D23V7, binary
                cls
clus               0   1
  RPTN MUTATED    37   3
  RPTN WILD-TYPE 219  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     37    3
  RPTN WILD-TYPE  219   14
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0           37            219
  1            3             14
[1] 2 2
[1] FALSE
D23V8, binary
                cls
clus              0  1
  RPTN MUTATED   19  4
  RPTN WILD-TYPE 88 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     19    4
  RPTN WILD-TYPE   88   69
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO            19             88
  YES            4             69
[1] 2 2
[1] FALSE
D23V9, binary
                cls
clus               0   1
  RPTN MUTATED    10  32
  RPTN WILD-TYPE  27 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     10   32
  RPTN WILD-TYPE   27  221
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO            10             27
  YES           32            221
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, binary
                cls
clus               0   1
  RPTN MUTATED    15  27
  RPTN WILD-TYPE  94 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     15   27
  RPTN WILD-TYPE   94  154
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  FEMALE           15             94
  MALE             27            154
[1] 2 2
[1] FALSE
D23V12, binary
                cls
clus               0   1
  RPTN MUTATED    38   4
  RPTN WILD-TYPE 216  31
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     38    4
  RPTN WILD-TYPE  216   31
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO            38            216
  YES            4             31
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED       0                         0    42
  RPTN WILD-TYPE     5                         1   242
D23V13, multiclass
                           clus
vv                          RPTN MUTATED RPTN WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               42            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"
D23V14, binary
                cls
clus               0   1
  RPTN MUTATED     0  41
  RPTN WILD-TYPE   3 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      0   41
  RPTN WILD-TYPE    3  242
                        clus
vv                       RPTN MUTATED RPTN WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           41            242
[1] 2 2
[1] FALSE

Clustering(24) Variable = KRTAP5-10 MUTATION ANALYSIS
D24V1, survival
                     sevent
clus2                  0  1
  KRTAP5-10 MUTATED    2  4
  KRTAP5-10 WILD-TYPE 95 99
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                  6                 194 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                  4                  99 
$`KRTAP5-10 MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A2JN TCGA-EE-A29D TCGA-EE-A2MF TCGA-OD-A75X 
      134.40        36.85        64.83        12.99       209.79       297.01 

$`KRTAP5-10 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
      107.61        36.30       171.58        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
       81.99       103.13        15.25         5.75        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-QB-A6FS 
       42.48         7.59       120.53        34.49        46.92         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
              12.99                0.00 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
             297.01              346.49 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
             99.615              47.050 
[1] "13.0 - 297.0 (99.6)" "0.0 - 346.5 (47.0)" 
[1] "hr=" "1.5"
D24V2, survival
                     sevent
clus2                   0   1
  KRTAP5-10 MUTATED     2   8
  KRTAP5-10 WILD-TYPE 122 152
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                 10                 274 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
                  8                 152 
$`KRTAP5-10 MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A2JN TCGA-DA-A1I8 TCGA-EE-A29D TCGA-EE-A2MF 
      134.40        36.95        66.48        53.92        13.97       268.73 
TCGA-EE-A2MH TCGA-EE-A3JA TCGA-ER-A19E TCGA-OD-A75X 
       16.96        53.19        13.02       297.90 

$`KRTAP5-10 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       126.81        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      222.51       176.55        35.93       135.02        88.87        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20       204.66        96.23       180.39       216.66 
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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        51.35       134.33       152.81 
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-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
              13.02                0.20 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
             297.90              369.93 
  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE 
             53.555              54.215 
[1] "13.0 - 297.9 (53.6)" "0.2 - 369.9 (54.2)" 
[1] "hr=" "1.1"
D24V3, continuous
                     vv
clus                  I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  KRTAP5-10 MUTATED          0       0       2        0        2        0
  KRTAP5-10 WILD-TYPE       10       6      23       10       23       18
                     vv
clus                  STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  KRTAP5-10 MUTATED           0         0         1         3          0
  KRTAP5-10 WILD-TYPE        10        14         9        33         14
                     vv
clus                  STAGE IIIB STAGE IIIC STAGE IV
  KRTAP5-10 MUTATED            0          1        0
  KRTAP5-10 WILD-TYPE         26         42       16
D24V4, multiclass
            clus
vv           KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  I/II NOS                   0                  10
  STAGE 0                    0                   6
  STAGE I                    2                  23
  STAGE IA                   0                  10
  STAGE IB                   2                  23
  STAGE II                   0                  18
  STAGE IIA                  0                  10
  STAGE IIB                  0                  14
  STAGE IIC                  1                   9
  STAGE III                  3                  33
  STAGE IIIA                 0                  14
  STAGE IIIB                 0                  26
  STAGE IIIC                 1                  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
  KRTAP5-10 MUTATED       1  4  1  2
  KRTAP5-10 WILD-TYPE    52 58 59 53
D24V5, multiclass
       clus
vv      KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  T0+T1                 1                  52
  T2                    4                  58
  T3                    1                  59
  T4                    2                  53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  KRTAP5-10 MUTATED     6   2   1   0
  KRTAP5-10 WILD-TYPE 137  51  33  35
D24V6, multiclass
    clus
vv   KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  N0                 6                 137
  N1                 2                  51
  N2                 1                  33
  N3                 0                  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"
D24V7, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED    10   0
  KRTAP5-10 WILD-TYPE 246  17
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED     10    0
  KRTAP5-10 WILD-TYPE  246   17
   clus
vv  KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  0                10                 246
  1                 0                  17
[1] 2 2
[1] FALSE
D24V8, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED     4   2
  KRTAP5-10 WILD-TYPE 103  71
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      4    2
  KRTAP5-10 WILD-TYPE  103   71
     clus
vv    KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  NO                  4                 103
  YES                 2                  71
[1] 2 2
[1] FALSE
D24V9, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED     1   9
  KRTAP5-10 WILD-TYPE  36 244
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      1    9
  KRTAP5-10 WILD-TYPE   36  244
     clus
vv    KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  NO                  1                  36
  YES                 9                 244
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED     4   6
  KRTAP5-10 WILD-TYPE 105 175
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      4    6
  KRTAP5-10 WILD-TYPE  105  175
        clus
vv       KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  FEMALE                 4                 105
  MALE                   6                 175
[1] 2 2
[1] FALSE
D24V12, binary
                     cls
clus                    0   1
  KRTAP5-10 MUTATED     9   1
  KRTAP5-10 WILD-TYPE 245  34
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      9    1
  KRTAP5-10 WILD-TYPE  245   34
     clus
vv    KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  NO                  9                 245
  YES                 1                  34
[1] 2 2
[1] FALSE
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-10 MUTATED       0                         0    10
  KRTAP5-10 WILD-TYPE     5                         1   274
D24V13, multiclass
                           clus
vv                          KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  ASIAN                                     0                   5
  BLACK OR AFRICAN AMERICAN                 0                   1
  WHITE                                    10                 274
[1] 3 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
  KRTAP5-10 MUTATED     0  10
  KRTAP5-10 WILD-TYPE   3 273
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-10 MUTATED      0   10
  KRTAP5-10 WILD-TYPE    3  273
                        clus
vv                       KRTAP5-10 MUTATED KRTAP5-10 WILD-TYPE
  HISPANIC OR LATINO                     0                   3
  NOT HISPANIC OR LATINO                10                 273
[1] 2 2
[1] FALSE

Clustering(25) Variable = GML MUTATION ANALYSIS
D25V1, survival
               sevent
clus2            0  1
  GML MUTATED    3  5
  GML WILD-TYPE 94 98
  GML MUTATED GML WILD-TYPE 
            8           192 
  GML MUTATED GML WILD-TYPE 
            5            98 
$`GML MUTATED`
TCGA-D3-A2JC TCGA-DA-A1I7 TCGA-EE-A29D TCGA-EE-A2GJ TCGA-EE-A2MI TCGA-EE-A2MJ 
       86.30        60.10        12.99        68.65       171.85        63.25 
TCGA-EE-A2MT TCGA-FS-A1Z3 
       23.51         8.35 

$`GML WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       68.68       150.61       110.53        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
       30.02        77.98        26.14        12.95       201.60        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       94.19        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      174.21       171.78        49.74       195.98        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  GML MUTATED GML WILD-TYPE 
         8.35          0.00 
  GML MUTATED GML WILD-TYPE 
       171.85        346.49 
  GML MUTATED GML WILD-TYPE 
       61.675        47.050 
[1] "8.3 - 171.8 (61.7)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.3"
D25V2, survival
               sevent
clus2             0   1
  GML MUTATED     5   6
  GML WILD-TYPE 119 154
  GML MUTATED GML WILD-TYPE 
           11           273 
  GML MUTATED GML WILD-TYPE 
            6           154 
$`GML MUTATED`
TCGA-D3-A2JC TCGA-D9-A1JW TCGA-DA-A1I7 TCGA-EB-A5UL TCGA-EE-A29D TCGA-EE-A2GJ 
       86.76         3.65        88.87        29.29        13.97       107.38 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-FS-A1Z3 TCGA-GN-A4U7 
      204.66        96.23        71.21        20.91        10.42 

$`GML WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       20.38       222.51       176.55        35.93       135.02        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       43.36        13.87        10.36        20.35        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24        48.72        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        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       180.39       216.66       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-A3AG 
      122.73        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
      121.91        39.35        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  GML MUTATED GML WILD-TYPE 
         3.65          0.20 
  GML MUTATED GML WILD-TYPE 
       204.66        369.93 
  GML MUTATED GML WILD-TYPE 
        71.21         53.92 
[1] "3.6 - 204.7 (71.2)" "0.2 - 369.9 (53.9)"
[1] "hr=" "1.1"
D25V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  GML MUTATED          0       0       0        1        1        0         0
  GML WILD-TYPE       10       6      25        9       24       18        10
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GML MUTATED           1         0         3          0          1          2
  GML WILD-TYPE        13        10        33         14         25         41
               vv
clus            STAGE IV
  GML MUTATED          1
  GML WILD-TYPE       15
D25V4, multiclass
            clus
vv           GML MUTATED GML WILD-TYPE
  I/II NOS             0            10
  STAGE 0              0             6
  STAGE I              0            25
  STAGE IA             1             9
  STAGE IB             1            24
  STAGE II             0            18
  STAGE IIA            0            10
  STAGE IIB            1            13
  STAGE IIC            0            10
  STAGE III            3            33
  STAGE IIIA           0            14
  STAGE IIIB           1            25
  STAGE IIIC           2            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
  GML MUTATED       4  2  1  2
  GML WILD-TYPE    49 60 59 53
D25V5, multiclass
       clus
vv      GML MUTATED GML WILD-TYPE
  T0+T1           4            49
  T2              2            60
  T3              1            59
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  GML MUTATED     5   2   3   1
  GML WILD-TYPE 138  51  31  34
D25V6, multiclass
    clus
vv   GML MUTATED GML WILD-TYPE
  N0           5           138
  N1           2            51
  N2           3            31
  N3           1            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"
D25V7, binary
               cls
clus              0   1
  GML MUTATED    10   1
  GML WILD-TYPE 246  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED     10    1
  GML WILD-TYPE  246   16
   clus
vv  GML MUTATED GML WILD-TYPE
  0          10           246
  1           1            16
[1] 2 2
[1] FALSE
D25V8, binary
               cls
clus              0   1
  GML MUTATED     5   1
  GML WILD-TYPE 102  72
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      5    1
  GML WILD-TYPE  102   72
     clus
vv    GML MUTATED GML WILD-TYPE
  NO            5           102
  YES           1            72
[1] 2 2
[1] FALSE
D25V9, binary
               cls
clus              0   1
  GML MUTATED     3   8
  GML WILD-TYPE  34 245
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      3    8
  GML WILD-TYPE   34  245
     clus
vv    GML MUTATED GML WILD-TYPE
  NO            3            34
  YES           8           245
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, binary
               cls
clus              0   1
  GML MUTATED     3   8
  GML WILD-TYPE 106 173
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      3    8
  GML WILD-TYPE  106  173
        clus
vv       GML MUTATED GML WILD-TYPE
  FEMALE           3           106
  MALE             8           173
[1] 2 2
[1] FALSE
D25V12, binary
               cls
clus              0   1
  GML MUTATED    10   1
  GML WILD-TYPE 244  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED     10    1
  GML WILD-TYPE  244   34
     clus
vv    GML MUTATED GML WILD-TYPE
  NO           10           244
  YES           1            34
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GML MUTATED       0                         0    11
  GML WILD-TYPE     5                         1   273
D25V13, multiclass
                           clus
vv                          GML MUTATED GML WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              11           273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
               cls
clus              0   1
  GML MUTATED     0  11
  GML WILD-TYPE   3 272
[1] "tbl2"
               cls
clus            [,1] [,2]
  GML MUTATED      0   11
  GML WILD-TYPE    3  272
                        clus
vv                       GML MUTATED GML WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          11           272
[1] 2 2
[1] FALSE

Clustering(26) Variable = MAP2K1 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     8   3
  MAP2K1 WILD-TYPE  89 100
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              11              189 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               3              100 
$`MAP2K1 MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A51F TCGA-EB-A5UN TCGA-EE-A29M TCGA-EE-A29T 
       49.35        19.04        30.67        52.41        47.74       346.49 
TCGA-EE-A2MU TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A42L TCGA-OD-A75X 
       53.26       168.85        19.86        74.47       297.01 

$`MAP2K1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       15.72        31.89       110.93       133.25        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21        23.67       173.85       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       42.64         3.91        16.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       76.14        12.99         0.26        44.28        47.41        27.16 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI 
        6.28        67.89       111.85        45.90         3.35       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       15.48        32.05         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           19.04             0.00 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          346.49           312.07 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           52.41            45.99 
[1] "19.0 - 346.5 (52.4)" "0.0 - 312.1 (46.0)" 
[1] "hr=" "3.7"
D26V2, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED    11   4
  MAP2K1 WILD-TYPE 113 156
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              15              269 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               4              156 
$`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        58.92 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2M5 TCGA-EE-A2MU TCGA-EE-A3JB 
       56.84        14.47       369.93        21.67        53.26       201.80 
TCGA-EE-A3JH TCGA-ER-A42L TCGA-OD-A75X 
      134.33       149.03       297.90 

$`MAP2K1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67       112.04       112.57       133.25        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
      103.59        39.75       174.84        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       10.36        20.35        29.29         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       78.97        13.97        63.78        72.07        64.64        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        66.74        61.28        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        53.19        51.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21        12.95        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13         7.23         0.20         0.33         0.69 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           14.47             0.20 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          369.93           357.37 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           56.84            53.19 
[1] "14.5 - 369.9 (56.8)" "0.2 - 357.4 (53.2)" 
[1] "hr=" "3.5"
D26V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MAP2K1 MUTATED          0       0       1        1        2        1
  MAP2K1 WILD-TYPE       10       6      24        9       23       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MAP2K1 MUTATED           0         0         1         2          0
  MAP2K1 WILD-TYPE        10        14         9        34         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAP2K1 MUTATED            1          2        1
  MAP2K1 WILD-TYPE         25         41       15
D26V4, multiclass
            clus
vv           MAP2K1 MUTATED MAP2K1 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                1                9
  STAGE IB                2               23
  STAGE II                1               17
  STAGE IIA               0               10
  STAGE IIB               0               14
  STAGE IIC               1                9
  STAGE III               2               34
  STAGE IIIA              0               14
  STAGE IIIB              1               25
  STAGE IIIC              2               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
  MAP2K1 MUTATED       2  4  3  3
  MAP2K1 WILD-TYPE    51 58 57 52
D26V5, multiclass
       clus
vv      MAP2K1 MUTATED MAP2K1 WILD-TYPE
  T0+T1              2               51
  T2                 4               58
  T3                 3               57
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP2K1 MUTATED     5   5   1   1
  MAP2K1 WILD-TYPE 138  48  33  34
D26V6, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  N0              5              138
  N1              5               48
  N2              1               33
  N3              1               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"
D26V7, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED    14   1
  MAP2K1 WILD-TYPE 242  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED     14    1
  MAP2K1 WILD-TYPE  242   16
   clus
vv  MAP2K1 MUTATED MAP2K1 WILD-TYPE
  0             14              242
  1              1               16
[1] 2 2
[1] FALSE
D26V8, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     5   4
  MAP2K1 WILD-TYPE 102  69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      5    4
  MAP2K1 WILD-TYPE  102   69
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               5              102
  YES              4               69
[1] 2 2
[1] FALSE
D26V9, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     1  14
  MAP2K1 WILD-TYPE  36 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      1   14
  MAP2K1 WILD-TYPE   36  239
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               1               36
  YES             14              239
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     6   9
  MAP2K1 WILD-TYPE 103 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      6    9
  MAP2K1 WILD-TYPE  103  172
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  FEMALE              6              103
  MALE                9              172
[1] 2 2
[1] FALSE
D26V12, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED    14   1
  MAP2K1 WILD-TYPE 240  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED     14    1
  MAP2K1 WILD-TYPE  240   34
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO              14              240
  YES              1               34
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP2K1 MUTATED       0                         0    15
  MAP2K1 WILD-TYPE     5                         1   269
D26V13, multiclass
                           clus
vv                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 15              269
[1] 3 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
  MAP2K1 MUTATED     0  15
  MAP2K1 WILD-TYPE   3 268
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      0   15
  MAP2K1 WILD-TYPE    3  268
                        clus
vv                       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             15              268
[1] 2 2
[1] FALSE

Clustering(27) Variable = IDH1 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2             0  1
  IDH1 MUTATED    4  6
  IDH1 WILD-TYPE 93 97
  IDH1 MUTATED IDH1 WILD-TYPE 
            10            190 
  IDH1 MUTATED IDH1 WILD-TYPE 
             6             97 
$`IDH1 MUTATED`
TCGA-D9-A3Z1 TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A2GU TCGA-EE-A3J8 TCGA-EE-A3JI 
       15.02        75.22        27.16        81.99         3.35       135.98 
TCGA-ER-A3ES TCGA-ER-A42L TCGA-GN-A268 TCGA-RP-A693 
      173.29        74.47        42.48         0.33 

$`IDH1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       71.31       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       45.90       168.85        19.86        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       28.67        68.52        15.48        32.05         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        96.92        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       46.92       297.01         7.23         0.20 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.33           0.00 
  IDH1 MUTATED IDH1 WILD-TYPE 
        173.29         346.49 
  IDH1 MUTATED IDH1 WILD-TYPE 
        58.475         47.295 
[1] "0.3 - 173.3 (58.5)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.2"
D27V2, survival
                sevent
clus2              0   1
  IDH1 MUTATED     6   8
  IDH1 WILD-TYPE 118 152
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            270 
  IDH1 MUTATED IDH1 WILD-TYPE 
             8            152 
$`IDH1 MUTATED`
TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A3Z1 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29P 
      137.92        54.67        15.39        63.35        85.08        56.42 
TCGA-EE-A2GU TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A3ES TCGA-ER-A42L TCGA-FS-A1ZP 
       94.82        34.32       152.81       247.04       149.03        74.73 
TCGA-GN-A268 TCGA-RP-A693 
       62.79         0.33 

$`IDH1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       125.79       135.75       178.32        18.18       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      151.53         3.65         7.10        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       13.55        78.97        13.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        66.74        14.47        61.28       369.93 
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       115.96        59.64 
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       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       13.91        42.77        81.21        44.88        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       180.39       216.66 
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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       64.08        53.19       201.80        51.35       134.33        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       48.99        41.56        93.01        46.98        33.21        12.95 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A694 
       48.89        22.13       297.90         7.23         0.20         0.69 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.33           0.20 
  IDH1 MUTATED IDH1 WILD-TYPE 
        247.04         369.93 
  IDH1 MUTATED IDH1 WILD-TYPE 
        69.040         53.175 
[1] "0.3 - 247.0 (69.0)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.2"
D27V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  IDH1 MUTATED          0       0       1        1        0        3         0
  IDH1 WILD-TYPE       10       6      24        9       25       15        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  IDH1 MUTATED           2         1         0          2          0          1
  IDH1 WILD-TYPE        12         9        36         12         26         42
                vv
clus             STAGE IV
  IDH1 MUTATED          2
  IDH1 WILD-TYPE       14
D27V4, multiclass
            clus
vv           IDH1 MUTATED IDH1 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               1             24
  STAGE IA              1              9
  STAGE IB              0             25
  STAGE II              3             15
  STAGE IIA             0             10
  STAGE IIB             2             12
  STAGE IIC             1              9
  STAGE III             0             36
  STAGE IIIA            2             12
  STAGE IIIB            0             26
  STAGE IIIC            1             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
  IDH1 MUTATED       1  2  4  4
  IDH1 WILD-TYPE    52 60 56 51
D27V5, multiclass
       clus
vv      IDH1 MUTATED IDH1 WILD-TYPE
  T0+T1            1             52
  T2               2             60
  T3               4             56
  T4               4             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IDH1 MUTATED     8   3   0   1
  IDH1 WILD-TYPE 135  50  34  34
D27V6, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  N0            8            135
  N1            3             50
  N2            0             34
  N3            1             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"
D27V7, binary
                cls
clus               0   1
  IDH1 MUTATED    12   2
  IDH1 WILD-TYPE 244  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     12    2
  IDH1 WILD-TYPE  244   15
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0           12            244
  1            2             15
[1] 2 2
[1] FALSE
D27V8, binary
                cls
clus               0   1
  IDH1 MUTATED     7   2
  IDH1 WILD-TYPE 100  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      7    2
  IDH1 WILD-TYPE  100   71
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             7            100
  YES            2             71
[1] 2 2
[1] FALSE
D27V9, binary
                cls
clus               0   1
  IDH1 MUTATED     1  14
  IDH1 WILD-TYPE  36 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      1   14
  IDH1 WILD-TYPE   36  239
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             1             36
  YES           14            239
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, binary
                cls
clus               0   1
  IDH1 MUTATED     4  11
  IDH1 WILD-TYPE 105 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      4   11
  IDH1 WILD-TYPE  105  170
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            4            105
  MALE             11            170
[1] 2 2
[1] FALSE
D27V12, binary
                cls
clus               0   1
  IDH1 MUTATED    14   1
  IDH1 WILD-TYPE 240  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     14    1
  IDH1 WILD-TYPE  240   34
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO            14            240
  YES            1             34
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         0    15
  IDH1 WILD-TYPE     5                         1   269
D27V13, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               15            269
[1] 3 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
  IDH1 MUTATED     0  14
  IDH1 WILD-TYPE   3 269
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   14
  IDH1 WILD-TYPE    3  269
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           14            269
[1] 2 2
[1] FALSE

Clustering(28) Variable = KEL MUTATION ANALYSIS
D28V1, survival
               sevent
clus2            0  1
  KEL MUTATED   15 10
  KEL WILD-TYPE 82 93
  KEL MUTATED KEL WILD-TYPE 
           25           175 
  KEL MUTATED KEL WILD-TYPE 
           10            93 
$`KEL MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A2JL TCGA-D3-A3MR TCGA-D9-A6EC 
       62.07       134.40        36.85       171.58        90.21        69.21 
TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29C 
       42.64        52.41        13.15        20.38         0.00        76.14 
TCGA-EE-A29D TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AF 
       12.99         0.20        81.99        63.25        23.51         6.28 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FW-A3TV 
      135.98        34.45        32.05        74.47       174.21        11.54 
TCGA-GN-A265 
       96.92 

$`KEL WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       27.35        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       36.30        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        59.70        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV 
       45.70       177.86        15.02        22.29        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 
       58.85        30.44       225.11         3.91        16.41        18.21 
TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29E 
       24.89        26.24        75.55        79.20        75.22         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.76        71.31       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01       143.93        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
        4.41        54.51        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      168.85        19.86        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       68.52        15.48         4.50       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        80.68        55.59        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        1.91        53.29       117.93        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  KEL MUTATED KEL WILD-TYPE 
          0.0           0.2 
  KEL MUTATED KEL WILD-TYPE 
       174.21        346.49 
  KEL MUTATED KEL WILD-TYPE 
        52.41         47.18 
[1] "0.0 - 174.2 (52.4)" "0.2 - 346.5 (47.2)"
[1] "hr=" "1.2"
D28V2, survival
               sevent
clus2             0   1
  KEL MUTATED    19  17
  KEL WILD-TYPE 105 143
  KEL MUTATED KEL WILD-TYPE 
           36           248 
  KEL MUTATED KEL WILD-TYPE 
           17           143 
$`KEL MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EE-A2MR TCGA-ER-A198 TCGA-FW-A3R5 TCGA-D3-A2JL 
       62.07        13.87       134.40        50.76        36.95       171.58 
TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EB-A5UN 
      103.59       137.92        77.56        43.36        29.29        58.92 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A2GI 
       29.82        33.73        14.70        78.97        13.97        48.72 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AF 
       42.77        94.82        47.28        96.23        71.21        13.81 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A3PL 
       41.59        36.95        53.19       152.81        35.44        33.21 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
      149.03       174.21        13.51        15.78        96.92        10.13 

$`KEL WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       46.32        68.25        54.02        94.98        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FS-A1ZF 
        2.60       340.14       126.81        27.35        31.40        15.45 
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        66.48        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-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-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      125.79       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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       13.87        10.36        20.35         7.04        36.46        27.22 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        8.65        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        85.08        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        81.21        44.88        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       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       28.77        54.51       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 
       34.32       201.80        51.35       134.33        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P 
      247.04        93.01        46.98        12.95        92.98        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        19.43         2.04       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  KEL MUTATED KEL WILD-TYPE 
        10.13          0.20 
  KEL MUTATED KEL WILD-TYPE 
       174.21        369.93 
  KEL MUTATED KEL WILD-TYPE 
        48.00         54.59 
[1] "10.1 - 174.2 (48.0)" "0.2 - 369.9 (54.6)" 
[1] "hr=" "1"  
D28V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KEL MUTATED          1       0       2        4        3        6         0
  KEL WILD-TYPE        9       6      23        6       22       12        10
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KEL MUTATED           0         1         6          2          3          3
  KEL WILD-TYPE        14         9        30         12         23         40
               vv
clus            STAGE IV
  KEL MUTATED          1
  KEL WILD-TYPE       15
D28V4, multiclass
            clus
vv           KEL MUTATED KEL WILD-TYPE
  I/II NOS             1             9
  STAGE 0              0             6
  STAGE I              2            23
  STAGE IA             4             6
  STAGE IB             3            22
  STAGE II             6            12
  STAGE IIA            0            10
  STAGE IIB            0            14
  STAGE IIC            1             9
  STAGE III            6            30
  STAGE IIIA           2            12
  STAGE IIIB           3            23
  STAGE IIIC           3            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
  KEL MUTATED       8  6  8  6
  KEL WILD-TYPE    45 56 52 49
D28V5, multiclass
       clus
vv      KEL MUTATED KEL WILD-TYPE
  T0+T1           8            45
  T2              6            56
  T3              8            52
  T4              6            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  KEL MUTATED    19   6   5   1
  KEL WILD-TYPE 124  47  29  34
D28V6, multiclass
    clus
vv   KEL MUTATED KEL WILD-TYPE
  N0          19           124
  N1           6            47
  N2           5            29
  N3           1            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"
D28V7, binary
               cls
clus              0   1
  KEL MUTATED    32   1
  KEL WILD-TYPE 224  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED     32    1
  KEL WILD-TYPE  224   16
   clus
vv  KEL MUTATED KEL WILD-TYPE
  0          32           224
  1           1            16
[1] 2 2
[1] FALSE
D28V8, binary
               cls
clus             0  1
  KEL MUTATED   16  6
  KEL WILD-TYPE 91 67
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED     16    6
  KEL WILD-TYPE   91   67
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO           16            91
  YES           6            67
[1] 2 2
[1] FALSE
D28V9, binary
               cls
clus              0   1
  KEL MUTATED     6  30
  KEL WILD-TYPE  31 223
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      6   30
  KEL WILD-TYPE   31  223
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO            6            31
  YES          30           223
[1] 2 2
[1] FALSE
D28V10, continuous
D28V11, binary
               cls
clus              0   1
  KEL MUTATED     7  29
  KEL WILD-TYPE 102 152
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      7   29
  KEL WILD-TYPE  102  152
        clus
vv       KEL MUTATED KEL WILD-TYPE
  FEMALE           7           102
  MALE            29           152
[1] 2 2
[1] FALSE
D28V12, binary
               cls
clus              0   1
  KEL MUTATED    29   7
  KEL WILD-TYPE 225  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED     29    7
  KEL WILD-TYPE  225   28
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO           29           225
  YES           7            28
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KEL MUTATED       0                         0    36
  KEL WILD-TYPE     5                         1   248
D28V13, multiclass
                           clus
vv                          KEL MUTATED KEL WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              36           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"
D28V14, binary
               cls
clus              0   1
  KEL MUTATED     0  35
  KEL WILD-TYPE   3 248
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      0   35
  KEL WILD-TYPE    3  248
                        clus
vv                       KEL MUTATED KEL WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          35           248
[1] 2 2
[1] FALSE

Clustering(29) Variable = RQCD1 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  RQCD1 MUTATED     4   3
  RQCD1 WILD-TYPE  93 100
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              7             193 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              3             100 
$`RQCD1 MUTATED`
TCGA-D9-A6EC TCGA-EE-A29P TCGA-EE-A2GM TCGA-EE-A2GS TCGA-ER-A19P TCGA-FR-A3YN 
       69.21        27.16        18.35        71.31       120.76         4.50 
TCGA-FS-A1ZU 
        4.47 

$`RQCD1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        15.02        22.29        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        10.62        32.48        93.63         0.76         0.20 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84        42.51        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       74.47       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       130.95       136.27        35.28        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  RQCD1 MUTATED RQCD1 WILD-TYPE 
           4.47            0.00 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
         120.76          346.49 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
          27.16           47.41 
[1] "4.5 - 120.8 (27.2)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.2"
D29V2, survival
                 sevent
clus2               0   1
  RQCD1 MUTATED     5   3
  RQCD1 WILD-TYPE 119 157
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              8             276 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
              3             157 
$`RQCD1 MUTATED`
TCGA-D9-A6EC TCGA-EE-A29P TCGA-EE-A2GM TCGA-EE-A2GS TCGA-ER-A19P TCGA-FR-A3YN 
       77.56        56.42        75.48        81.21       162.08        92.98 
TCGA-FS-A1ZU TCGA-RP-A694 
       26.56         0.69 

$`RQCD1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29         9.90        25.18        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       54.74        79.66       102.12        13.91        42.77        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       180.39       216.66       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 
       64.04        28.77        54.51        13.81        41.59       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-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 

  RQCD1 MUTATED RQCD1 WILD-TYPE 
           0.69            0.20 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
         162.08          369.93 
  RQCD1 MUTATED RQCD1 WILD-TYPE 
          76.52           53.39 
[1] "0.7 - 162.1 (76.5)" "0.2 - 369.9 (53.4)"
[1] "hr=" "1.5"
D29V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  RQCD1 MUTATED          0       1       0        0        2        0         0
  RQCD1 WILD-TYPE       10       5      25       10       23       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RQCD1 MUTATED           0         3         0          1          0
  RQCD1 WILD-TYPE        14         7        36         13         26
                 vv
clus              STAGE IIIC STAGE IV
  RQCD1 MUTATED            0        1
  RQCD1 WILD-TYPE         43       15
D29V4, multiclass
            clus
vv           RQCD1 MUTATED RQCD1 WILD-TYPE
  I/II NOS               0              10
  STAGE 0                1               5
  STAGE I                0              25
  STAGE IA               0              10
  STAGE IB               2              23
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              3               7
  STAGE III              0              36
  STAGE IIIA             1              13
  STAGE IIIB             0              26
  STAGE IIIC             0              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
  RQCD1 MUTATED       0  2  1  3
  RQCD1 WILD-TYPE    53 60 59 52
D29V5, multiclass
       clus
vv      RQCD1 MUTATED RQCD1 WILD-TYPE
  T0+T1             0              53
  T2                2              60
  T3                1              59
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RQCD1 MUTATED     7   1   0   0
  RQCD1 WILD-TYPE 136  52  34  35
D29V6, multiclass
    clus
vv   RQCD1 MUTATED RQCD1 WILD-TYPE
  N0             7             136
  N1             1              52
  N2             0              34
  N3             0              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"
D29V7, binary
                 cls
clus                0   1
  RQCD1 MUTATED     8   1
  RQCD1 WILD-TYPE 248  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      8    1
  RQCD1 WILD-TYPE  248   16
   clus
vv  RQCD1 MUTATED RQCD1 WILD-TYPE
  0             8             248
  1             1              16
[1] 2 2
[1] FALSE
D29V8, binary
                 cls
clus                0   1
  RQCD1 MUTATED     3   3
  RQCD1 WILD-TYPE 104  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      3    3
  RQCD1 WILD-TYPE  104   70
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  NO              3             104
  YES             3              70
[1] 2 2
[1] FALSE
D29V9, binary
                 cls
clus                0   1
  RQCD1 MUTATED     1   8
  RQCD1 WILD-TYPE  36 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      1    8
  RQCD1 WILD-TYPE   36  245
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  NO              1              36
  YES             8             245
[1] 2 2
[1] FALSE
D29V10, continuous
D29V11, binary
                 cls
clus                0   1
  RQCD1 MUTATED     5   4
  RQCD1 WILD-TYPE 104 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      5    4
  RQCD1 WILD-TYPE  104  177
        clus
vv       RQCD1 MUTATED RQCD1 WILD-TYPE
  FEMALE             5             104
  MALE               4             177
[1] 2 2
[1] FALSE
D29V12, binary
                 cls
clus                0   1
  RQCD1 MUTATED     9   0
  RQCD1 WILD-TYPE 245  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      9    0
  RQCD1 WILD-TYPE  245   35
     clus
vv    RQCD1 MUTATED RQCD1 WILD-TYPE
  NO              9             245
  YES             0              35
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RQCD1 MUTATED       0                         0     9
  RQCD1 WILD-TYPE     5                         1   275
D29V13, multiclass
                           clus
vv                          RQCD1 MUTATED RQCD1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                 cls
clus                0   1
  RQCD1 MUTATED     0   9
  RQCD1 WILD-TYPE   3 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RQCD1 MUTATED      0    9
  RQCD1 WILD-TYPE    3  274
                        clus
vv                       RQCD1 MUTATED RQCD1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             274
[1] 2 2
[1] FALSE

Clustering(30) Variable = NGF MUTATION ANALYSIS
D30V1, survival
               sevent
clus2             0   1
  NGF MUTATED     4   1
  NGF WILD-TYPE  93 102
  NGF MUTATED NGF WILD-TYPE 
            5           195 
  NGF MUTATED NGF WILD-TYPE 
            1           102 
$`NGF MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A5GN TCGA-EB-A5UN TCGA-EE-A2MS TCGA-FS-A1ZZ 
      133.25        45.70        52.41       143.93         3.06 

$`NGF WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       15.72        31.89       110.93        49.35        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D9-A3Z1 
       31.76        62.70        11.34        42.05       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X 
      225.11        42.64         3.91        16.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  NGF MUTATED NGF WILD-TYPE 
         3.06          0.00 
  NGF MUTATED NGF WILD-TYPE 
       143.93        346.49 
  NGF MUTATED NGF WILD-TYPE 
        52.41         47.18 
[1] "3.1 - 143.9 (52.4)" "0.0 - 346.5 (47.2)"
[1] "hr=" "2.6"
D30V2, survival
               sevent
clus2             0   1
  NGF MUTATED     5   4
  NGF WILD-TYPE 119 156
  NGF MUTATED NGF WILD-TYPE 
            9           275 
  NGF MUTATED NGF WILD-TYPE 
            4           156 
$`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        58.92        61.28 
TCGA-EE-A2MS TCGA-FS-A1ZZ TCGA-GN-A266 
      162.48        27.02        10.13 

$`NGF WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.04       112.57        71.80        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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       65.92        40.60        68.09        33.93       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        10.36        20.35        29.29         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
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-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        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-A29T 
       56.84        18.61        56.42        66.74        14.47       369.93 
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       115.96        59.64 
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       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        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       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      216.66       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-A3AE 
       53.26       124.31       122.73        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  NGF MUTATED NGF WILD-TYPE 
        10.13          0.20 
  NGF MUTATED NGF WILD-TYPE 
       162.48        369.93 
  NGF MUTATED NGF WILD-TYPE 
        61.28         53.52 
[1] "10.1 - 162.5 (61.3)" "0.2 - 369.9 (53.5)" 
[1] "hr=" "1.3"
D30V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  NGF MUTATED          0       0       1        0        1        2         1
  NGF WILD-TYPE       10       6      24       10       24       16         9
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NGF MUTATED           1         1         0          0          1          0
  NGF WILD-TYPE        13         9        36         14         25         43
               vv
clus            STAGE IV
  NGF MUTATED          0
  NGF WILD-TYPE       16
D30V4, multiclass
            clus
vv           NGF MUTATED NGF WILD-TYPE
  I/II NOS             0            10
  STAGE 0              0             6
  STAGE I              1            24
  STAGE IA             0            10
  STAGE IB             1            24
  STAGE II             2            16
  STAGE IIA            1             9
  STAGE IIB            1            13
  STAGE IIC            1             9
  STAGE III            0            36
  STAGE IIIA           0            14
  STAGE IIIB           1            25
  STAGE IIIC           0            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
  NGF MUTATED       3  0  3  2
  NGF WILD-TYPE    50 62 57 53
D30V5, multiclass
       clus
vv      NGF MUTATED NGF WILD-TYPE
  T0+T1           3            50
  T2              0            62
  T3              3            57
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NGF MUTATED     6   0   1   0
  NGF WILD-TYPE 137  53  33  35
D30V6, multiclass
    clus
vv   NGF MUTATED NGF WILD-TYPE
  N0           6           137
  N1           0            53
  N2           1            33
  N3           0            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"
D30V7, binary
               cls
clus              0   1
  NGF MUTATED     8   0
  NGF WILD-TYPE 248  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      8    0
  NGF WILD-TYPE  248   17
   clus
vv  NGF MUTATED NGF WILD-TYPE
  0           8           248
  1           0            17
[1] 2 2
[1] FALSE
D30V8, binary
               cls
clus              0   1
  NGF MUTATED     3   2
  NGF WILD-TYPE 104  71
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    2
  NGF WILD-TYPE  104   71
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            3           104
  YES           2            71
[1] 2 2
[1] FALSE
D30V9, binary
               cls
clus              0   1
  NGF MUTATED     2   7
  NGF WILD-TYPE  35 246
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      2    7
  NGF WILD-TYPE   35  246
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            2            35
  YES           7           246
[1] 2 2
[1] FALSE
D30V10, continuous
D30V11, binary
               cls
clus              0   1
  NGF MUTATED     3   6
  NGF WILD-TYPE 106 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    6
  NGF WILD-TYPE  106  175
        clus
vv       NGF MUTATED NGF WILD-TYPE
  FEMALE           3           106
  MALE             6           175
[1] 2 2
[1] FALSE
D30V12, binary
               cls
clus              0   1
  NGF MUTATED     5   4
  NGF WILD-TYPE 249  31
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      5    4
  NGF WILD-TYPE  249   31
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            5           249
  YES           4            31
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NGF MUTATED       0                         0     9
  NGF WILD-TYPE     5                         1   275
D30V13, multiclass
                           clus
vv                          NGF MUTATED NGF WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               9           275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
               cls
clus              0   1
  NGF MUTATED     1   8
  NGF WILD-TYPE   2 275
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      1    8
  NGF WILD-TYPE    2  275
                        clus
vv                       NGF MUTATED NGF WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO           8           275
[1] 2 2
[1] FALSE

Clustering(31) Variable = DMC1 MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  DMC1 MUTATED     6   2
  DMC1 WILD-TYPE  91 101
  DMC1 MUTATED DMC1 WILD-TYPE 
             8            192 
  DMC1 MUTATED DMC1 WILD-TYPE 
             2            101 
$`DMC1 MUTATED`
TCGA-EB-A5SG TCGA-EE-A2MR TCGA-DA-A1I7 TCGA-EE-A29G TCGA-EE-A3J7 TCGA-ER-A19A 
       33.24       134.40        60.10        44.28        45.90         4.54 
TCGA-ER-A19M TCGA-GF-A3OT 
       59.84         9.90 

$`DMC1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        31.96       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       27.35        19.04        36.85         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61       110.53        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14        12.99         0.26        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       99.06        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       55.59        11.54        19.30        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  DMC1 MUTATED DMC1 WILD-TYPE 
          4.54           0.00 
  DMC1 MUTATED DMC1 WILD-TYPE 
        134.40         346.49 
  DMC1 MUTATED DMC1 WILD-TYPE 
        45.090         47.575 
[1] "4.5 - 134.4 (45.1)" "0.0 - 346.5 (47.6)"
[1] "hr=" "1.5"
D31V2, survival
                sevent
clus2              0   1
  DMC1 MUTATED     7   4
  DMC1 WILD-TYPE 117 156
  DMC1 MUTATED DMC1 WILD-TYPE 
            11            273 
  DMC1 MUTATED DMC1 WILD-TYPE 
             4            156 
$`DMC1 MUTATED`
TCGA-EB-A5SG TCGA-EE-A2MR TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-EE-A29A TCGA-EE-A29G 
       68.25       134.40        45.30        88.87        63.35        72.07 
TCGA-EE-A29S TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19M TCGA-GF-A3OT 
       61.28        64.08        77.75        61.05         9.90 

$`DMC1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        13.87        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         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-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      222.51       176.55        35.93       135.02        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        13.97        63.78        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        66.74        14.47       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66 
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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33       152.81 
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       302.07       152.35         6.44       131.51 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.35        10.42        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  DMC1 MUTATED DMC1 WILD-TYPE 
           9.9            0.2 
  DMC1 MUTATED DMC1 WILD-TYPE 
        134.40         369.93 
  DMC1 MUTATED DMC1 WILD-TYPE 
         64.08          53.19 
[1] "9.9 - 134.4 (64.1)" "0.2 - 369.9 (53.2)"
[1] "hr=" "1.5"
D31V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DMC1 MUTATED          0       0       2        0        1        0         1
  DMC1 WILD-TYPE       10       6      23       10       24       18         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DMC1 MUTATED           0         0         0          2          2          1
  DMC1 WILD-TYPE        14        10        36         12         24         42
                vv
clus             STAGE IV
  DMC1 MUTATED          1
  DMC1 WILD-TYPE       15
D31V4, multiclass
            clus
vv           DMC1 MUTATED DMC1 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               2             23
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              0             18
  STAGE IIA             1              9
  STAGE IIB             0             14
  STAGE IIC             0             10
  STAGE III             0             36
  STAGE IIIA            2             12
  STAGE IIIB            2             24
  STAGE IIIC            1             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
  DMC1 MUTATED       1  4  3  1
  DMC1 WILD-TYPE    52 58 57 54
D31V5, multiclass
       clus
vv      DMC1 MUTATED DMC1 WILD-TYPE
  T0+T1            1             52
  T2               4             58
  T3               3             57
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DMC1 MUTATED     5   1   3   1
  DMC1 WILD-TYPE 138  52  31  34
D31V6, multiclass
    clus
vv   DMC1 MUTATED DMC1 WILD-TYPE
  N0            5            138
  N1            1             52
  N2            3             31
  N3            1             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"
D31V7, binary
                cls
clus               0   1
  DMC1 MUTATED     9   1
  DMC1 WILD-TYPE 247  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      9    1
  DMC1 WILD-TYPE  247   16
   clus
vv  DMC1 MUTATED DMC1 WILD-TYPE
  0            9            247
  1            1             16
[1] 2 2
[1] FALSE
D31V8, binary
                cls
clus               0   1
  DMC1 MUTATED     6   2
  DMC1 WILD-TYPE 101  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      6    2
  DMC1 WILD-TYPE  101   71
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO             6            101
  YES            2             71
[1] 2 2
[1] FALSE
D31V9, binary
                cls
clus               0   1
  DMC1 MUTATED     2   9
  DMC1 WILD-TYPE  35 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      2    9
  DMC1 WILD-TYPE   35  244
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO             2             35
  YES            9            244
[1] 2 2
[1] FALSE
D31V10, continuous
D31V11, binary
                cls
clus               0   1
  DMC1 MUTATED     3   8
  DMC1 WILD-TYPE 106 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      3    8
  DMC1 WILD-TYPE  106  173
        clus
vv       DMC1 MUTATED DMC1 WILD-TYPE
  FEMALE            3            106
  MALE              8            173
[1] 2 2
[1] FALSE
D31V12, binary
                cls
clus               0   1
  DMC1 MUTATED    10   1
  DMC1 WILD-TYPE 244  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED     10    1
  DMC1 WILD-TYPE  244   34
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO            10            244
  YES            1             34
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DMC1 MUTATED       0                         0    11
  DMC1 WILD-TYPE     5                         1   273
D31V13, multiclass
                           clus
vv                          DMC1 MUTATED DMC1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               11            273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                cls
clus               0   1
  DMC1 MUTATED     0  10
  DMC1 WILD-TYPE   3 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      0   10
  DMC1 WILD-TYPE    3  273
                        clus
vv                       DMC1 MUTATED DMC1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           10            273
[1] 2 2
[1] FALSE

Clustering(32) Variable = TRERF1 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2               0  1
  TRERF1 MUTATED    9  8
  TRERF1 WILD-TYPE 88 95
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              17              183 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               8               95 
$`TRERF1 MUTATED`
TCGA-EB-A5SG TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-EE-A29D TCGA-EE-A29T 
       33.24       134.40        27.35        36.85        12.99       346.49 
TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2M6 TCGA-EE-A2MI TCGA-EE-A2MJ 
       30.02        68.65        10.62       103.13       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A3AA TCGA-FS-A1YW TCGA-FS-A4F8 TCGA-GN-A267 
       89.26       124.31       171.78       173.19        17.06 

$`TRERF1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        31.96       166.75       269.03        52.90 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       42.05        45.70       177.86        15.02        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14         0.26        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       61.12       185.19       115.43        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      201.60        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       71.31        81.99        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       94.19       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
           10.62             0.00 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          346.49           312.07 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           68.65            46.92 
[1] "10.6 - 346.5 (68.7)" "0.0 - 312.1 (46.9)" 
[1] "hr=" "1.6"
D32V2, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED    10  15
  TRERF1 WILD-TYPE 114 145
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              25              259 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              15              145 
$`TRERF1 MUTATED`
TCGA-EB-A5SG TCGA-EE-A29L TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-DA-A1I0 
       68.25         2.60       134.40        27.35        36.95        20.38 
TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2GJ 
       13.97        18.61        61.28       369.93        59.64       107.38 
TCGA-EE-A2GK TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       54.74       129.27        47.28       204.66        96.23       180.39 
TCGA-EE-A3AA TCGA-FS-A1YW TCGA-FS-A1ZP TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-GF-A6C9 
      124.31       216.92        74.73        28.73       174.84        15.78 
TCGA-GN-A267 
       64.44 

$`TRERF1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        13.87        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      168.26       340.14       126.81        31.40        50.76        15.45 
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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       76.57        36.03       144.89       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       78.97        63.78        72.07        64.64        56.84        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       66.74        14.47        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-A2GE 
      115.96        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      220.24        48.72        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
       42.77        81.21        44.88        94.82        21.67        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-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      216.66       167.90        47.54       248.65        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        92.98       174.21 
TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.72        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        46.45 
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-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.02        77.82        66.67        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       19.43         2.04       139.89       117.93        96.92        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
             2.6              0.2 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          369.93           357.37 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
           64.44            53.19 
[1] "2.6 - 369.9 (64.4)" "0.2 - 357.4 (53.2)"
[1] "hr=" "1.2"
D32V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  TRERF1 MUTATED          2       0       4        1        2        2
  TRERF1 WILD-TYPE        8       6      21        9       23       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  TRERF1 MUTATED           1         1         0         5          1
  TRERF1 WILD-TYPE         9        13        10        31         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  TRERF1 MUTATED            1          3        1
  TRERF1 WILD-TYPE         25         40       15
D32V4, multiclass
            clus
vv           TRERF1 MUTATED TRERF1 WILD-TYPE
  I/II NOS                2                8
  STAGE 0                 0                6
  STAGE I                 4               21
  STAGE IA                1                9
  STAGE IB                2               23
  STAGE II                2               16
  STAGE IIA               1                9
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               5               31
  STAGE IIIA              1               13
  STAGE IIIB              1               25
  STAGE IIIC              3               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
  TRERF1 MUTATED       6  3  4  7
  TRERF1 WILD-TYPE    47 59 56 48
D32V5, multiclass
       clus
vv      TRERF1 MUTATED TRERF1 WILD-TYPE
  T0+T1              6               47
  T2                 3               59
  T3                 4               56
  T4                 7               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TRERF1 MUTATED    15   3   3   2
  TRERF1 WILD-TYPE 128  50  31  33
D32V6, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  N0             15              128
  N1              3               50
  N2              3               31
  N3              2               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"
D32V7, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    23   1
  TRERF1 WILD-TYPE 233  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     23    1
  TRERF1 WILD-TYPE  233   16
   clus
vv  TRERF1 MUTATED TRERF1 WILD-TYPE
  0             23              233
  1              1               16
[1] 2 2
[1] FALSE
D32V8, binary
                  cls
clus                0  1
  TRERF1 MUTATED   10  5
  TRERF1 WILD-TYPE 97 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     10    5
  TRERF1 WILD-TYPE   97   68
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO              10               97
  YES              5               68
[1] 2 2
[1] FALSE
D32V9, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     3  23
  TRERF1 WILD-TYPE  34 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      3   23
  TRERF1 WILD-TYPE   34  230
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO               3               34
  YES             23              230
[1] 2 2
[1] FALSE
D32V10, continuous
D32V11, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     6  20
  TRERF1 WILD-TYPE 103 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      6   20
  TRERF1 WILD-TYPE  103  161
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE              6              103
  MALE               20              161
[1] 2 2
[1] FALSE
D32V12, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    24   2
  TRERF1 WILD-TYPE 230  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     24    2
  TRERF1 WILD-TYPE  230   33
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO              24              230
  YES              2               33
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRERF1 MUTATED       0                         0    26
  TRERF1 WILD-TYPE     5                         1   258
D32V13, multiclass
                           clus
vv                          TRERF1 MUTATED TRERF1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 26              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"
D32V14, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     0  26
  TRERF1 WILD-TYPE   3 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      0   26
  TRERF1 WILD-TYPE    3  257
                        clus
vv                       TRERF1 MUTATED TRERF1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             26              257
[1] 2 2
[1] FALSE

Clustering(33) Variable = CYP3A5 MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  CYP3A5 MUTATED     3   2
  CYP3A5 WILD-TYPE  94 101
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
               5              195 
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
               2              101 
$`CYP3A5 MUTATED`
TCGA-D3-A3MR TCGA-EE-A29E TCGA-EE-A2GE TCGA-FS-A1ZZ TCGA-OD-A75X 
       90.21         0.26        12.95         3.06       297.01 

$`CYP3A5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       75.55        79.20        75.22        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        30.02        77.98        26.14       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       35.28         4.47        23.21         5.29        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
            0.26             0.00 
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
          297.01           346.49 
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
           12.95            47.41 
[1] "0.3 - 297.0 (12.9)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.7"
D33V2, survival
                  sevent
clus2                0   1
  CYP3A5 MUTATED     5   8
  CYP3A5 WILD-TYPE 119 152
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
              13              271 
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
               8              152 
$`CYP3A5 MUTATED`
TCGA-FS-A1ZF TCGA-D3-A3MR TCGA-DA-A1HW TCGA-EE-A29E TCGA-EE-A29V TCGA-EE-A29X 
       15.45       103.59        36.03        63.78        25.87        17.92 
TCGA-EE-A2GE TCGA-ER-A2NH TCGA-FS-A1ZK TCGA-FS-A1ZZ TCGA-GF-A6C9 TCGA-GN-A4U7 
      173.79        41.56        23.93        27.02        15.78        10.42 
TCGA-OD-A75X 
      297.90 

$`CYP3A5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       27.35        31.40        50.76        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       166.52        86.93        60.23        24.53 
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-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        77.56        22.95        76.57       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       61.28       369.93       195.02        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
       39.29        86.14        59.28        67.43       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66 
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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        28.83        48.99       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        19.43         2.04       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       39.35        48.89        22.13         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
           10.42             0.20 
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
          297.90           369.93 
  CYP3A5 MUTATED CYP3A5 WILD-TYPE 
           27.02            54.51 
[1] "10.4 - 297.9 (27.0)" "0.2 - 369.9 (54.5)" 
[1] "hr=" "1.3"
D33V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CYP3A5 MUTATED          0       0       1        0        1        1
  CYP3A5 WILD-TYPE       10       6      24       10       24       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CYP3A5 MUTATED           0         1         1         1          0
  CYP3A5 WILD-TYPE        10        13         9        35         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CYP3A5 MUTATED            3          3        0
  CYP3A5 WILD-TYPE         23         40       16
D33V4, multiclass
            clus
vv           CYP3A5 MUTATED CYP3A5 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                0               10
  STAGE IB                1               24
  STAGE II                1               17
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               1                9
  STAGE III               1               35
  STAGE IIIA              0               14
  STAGE IIIB              3               23
  STAGE IIIC              3               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
  CYP3A5 MUTATED       2  3  4  2
  CYP3A5 WILD-TYPE    51 59 56 53
D33V5, multiclass
       clus
vv      CYP3A5 MUTATED CYP3A5 WILD-TYPE
  T0+T1              2               51
  T2                 3               59
  T3                 4               56
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CYP3A5 MUTATED     5   4   0   2
  CYP3A5 WILD-TYPE 138  49  34  33
D33V6, multiclass
    clus
vv   CYP3A5 MUTATED CYP3A5 WILD-TYPE
  N0              5              138
  N1              4               49
  N2              0               34
  N3              2               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"
D33V7, binary
                  cls
clus                 0   1
  CYP3A5 MUTATED    12   0
  CYP3A5 WILD-TYPE 244  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A5 MUTATED     12    0
  CYP3A5 WILD-TYPE  244   17
   clus
vv  CYP3A5 MUTATED CYP3A5 WILD-TYPE
  0             12              244
  1              0               17
[1] 2 2
[1] FALSE
D33V8, binary
                  cls
clus                 0   1
  CYP3A5 MUTATED     6   3
  CYP3A5 WILD-TYPE 101  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A5 MUTATED      6    3
  CYP3A5 WILD-TYPE  101   70
     clus
vv    CYP3A5 MUTATED CYP3A5 WILD-TYPE
  NO               6              101
  YES              3               70
[1] 2 2
[1] FALSE
D33V9, binary
                  cls
clus                 0   1
  CYP3A5 MUTATED     2  11
  CYP3A5 WILD-TYPE  35 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A5 MUTATED      2   11
  CYP3A5 WILD-TYPE   35  242
     clus
vv    CYP3A5 MUTATED CYP3A5 WILD-TYPE
  NO               2               35
  YES             11              242
[1] 2 2
[1] FALSE
D33V10, continuous
D33V11, binary
                  cls
clus                 0   1
  CYP3A5 MUTATED     5   8
  CYP3A5 WILD-TYPE 104 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A5 MUTATED      5    8
  CYP3A5 WILD-TYPE  104  173
        clus
vv       CYP3A5 MUTATED CYP3A5 WILD-TYPE
  FEMALE              5              104
  MALE                8              173
[1] 2 2
[1] FALSE
D33V12, binary
                  cls
clus                 0   1
  CYP3A5 MUTATED    10   3
  CYP3A5 WILD-TYPE 244  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A5 MUTATED     10    3
  CYP3A5 WILD-TYPE  244   32
     clus
vv    CYP3A5 MUTATED CYP3A5 WILD-TYPE
  NO              10              244
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP3A5 MUTATED       0                         0    13
  CYP3A5 WILD-TYPE     5                         1   271
D33V13, multiclass
                           clus
vv                          CYP3A5 MUTATED CYP3A5 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 13              271
[1] 3 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
  CYP3A5 MUTATED     1  12
  CYP3A5 WILD-TYPE   2 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A5 MUTATED      1   12
  CYP3A5 WILD-TYPE    2  271
                        clus
vv                       CYP3A5 MUTATED CYP3A5 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             12              271
[1] 2 2
[1] FALSE

Clustering(34) Variable = BRAF MUTATION ANALYSIS
D34V1, survival
                sevent
clus2             0  1
  BRAF MUTATED   56 43
  BRAF WILD-TYPE 41 60
  BRAF MUTATED BRAF WILD-TYPE 
            99            101 
  BRAF MUTATED BRAF WILD-TYPE 
            43             60 
$`BRAF MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q4 
      166.75        52.90        27.35        19.04        36.85        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2JG 
      110.93        49.35       133.25        76.41        45.99       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
       36.30        64.83        43.53        58.06       140.98        59.70 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51T 
        9.34        90.21        23.67        30.67       144.46        11.34 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       45.70       177.86        22.29        69.21        22.85       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UN 
      150.61       110.53        60.10       225.11        42.64        52.41 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       24.89        20.38        26.24        79.20        76.14         0.26 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 
       47.41        47.74        27.16       346.49       185.19        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GS 
       26.14        12.95       201.60        68.65        18.35        71.31 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
      103.13        15.25         5.75        94.19        89.26       227.01 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      124.31       122.73         4.41         6.28        67.89       111.85 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
      168.85        19.86        53.29        39.81       184.60       150.12 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND 
       59.84       120.76        49.71        47.18        22.36         4.70 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1YY TCGA-FS-A1ZC 
       28.67        32.05        74.47       174.21        49.74       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FW-A3TV 
       32.78        78.61       136.27         3.06       173.19        11.54 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26A 
       19.30        18.25         1.91        53.29        96.92         7.59 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       46.92       297.01         7.23 

$`BRAF WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        38.76        33.24        31.96       269.03       134.40 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
        8.42        15.72        19.04        62.60        25.64        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3CC 
       15.75       168.00        86.30       171.58        66.08        40.01 
TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A3Z1 
       24.53       173.85        31.76        62.70        42.05        15.02 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q 
       76.34        68.68        64.83        58.85        30.44         3.91 
TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29B 
       16.41        18.21        13.15         0.00        75.55        75.22 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GK 
       12.99        44.28        61.12       115.43        30.02        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC 
       32.48        93.63         0.76         0.20        81.99        23.77 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS 
      209.79       171.85        63.25       104.78       145.45       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.51        53.26        64.04        54.51        45.90         3.35 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
      135.98        34.45        10.49         7.82         4.54        11.47 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       99.06        42.51       146.63        73.05        16.87        10.19 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1Z0 
      173.29        68.52        15.48         4.50       171.78       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
        8.35        27.62        43.92         7.82        36.33       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       35.28         4.47        23.21         5.29        18.51        66.67 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A267 
       13.28        80.68        55.59         9.90       117.93        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-RP-A690 TCGA-RP-A693 
       42.48       120.53        34.49         0.20         0.33 

  BRAF MUTATED BRAF WILD-TYPE 
          0.26           0.00 
  BRAF MUTATED BRAF WILD-TYPE 
        346.49         269.03 
  BRAF MUTATED BRAF WILD-TYPE 
         52.90          40.01 
[1] "0.3 - 346.5 (52.9)" "0.0 - 269.0 (40.0)"
[1] "hr=" "1.9"
D34V2, survival
                sevent
clus2             0  1
  BRAF MUTATED   68 73
  BRAF WILD-TYPE 56 87
  BRAF MUTATED BRAF WILD-TYPE 
           141            143 
  BRAF MUTATED BRAF WILD-TYPE 
            73             87 
$`BRAF MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      168.26       126.81        27.35        31.40        50.76        15.45 
TCGA-FW-A3R5 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       36.95       112.04       112.57        71.80       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       90.90       103.10        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 
       66.48        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-D9-A6EG 
        3.65         7.10        22.29         9.90        77.56        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       144.89        20.38       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UN 
       88.87        53.92        40.60       225.96        43.36        58.92 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
       27.22        33.73        26.89       133.81        91.56        63.35 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       78.97        63.78        64.64        56.84        18.61        56.42 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      369.93       195.02        46.82        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GS TCGA-EE-A2GT 
      173.79       220.24       107.38        75.48        81.21        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       180.39       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 
       28.77        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
      201.80        51.35       134.33        98.40        48.89        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P 
       26.37       302.07       152.35         6.44        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL 
       50.89        49.48        43.82        23.34        48.99        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       12.95       149.03       174.21        48.59       228.59         7.79 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
      357.37        53.52        32.75       101.26        11.41       148.80 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO 
       27.02       174.84        26.73        13.51        19.30        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A4U7 
        2.04        15.78       139.89        96.92        32.48        10.42 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       48.89       297.90         7.23 

$`BRAF WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       68.15         2.60       340.14       134.40        16.57        16.67 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       28.08        95.74        43.43        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC 
      168.00        86.76       171.58        66.08       130.72        86.93 
TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
       24.53        45.30       174.84        56.35        32.94        63.81 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-DA-A1HV 
      125.79       137.92        54.67        15.39        25.18        76.57 
TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q 
      222.51        65.92        68.09        33.93        10.49        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       10.36        20.35        29.29         7.04        36.46        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B 
        8.65        14.70         4.96       151.27        13.55        85.08 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       13.97        72.07        66.74        14.47        61.28        25.87 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GK 
       17.92       115.96        59.64        39.29        48.72        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC 
       79.66       102.12        13.91        42.77        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       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AE 
       47.54       162.48        71.21        53.26        64.04        54.51 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A195 
       36.95        64.08        34.32        53.19       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N 
       13.94         9.17        77.75        12.59       131.51        44.09 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
        8.88       148.18       105.07        20.15        28.83        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW 
      247.04        93.01        46.98        92.98        15.72       216.92 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
      202.65        20.91        28.08        27.72        48.85        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
        9.70        47.38        23.93        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        77.82        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A3OT 
       34.03        54.41        80.68        17.46        55.59         9.90 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U3 
      117.93        10.13        64.44        62.79        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U9 TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       39.35        22.13         0.20         0.33         0.69 

  BRAF MUTATED BRAF WILD-TYPE 
          2.04           0.20 
  BRAF MUTATED BRAF WILD-TYPE 
        369.93         340.14 
  BRAF MUTATED BRAF WILD-TYPE 
         56.84          53.16 
[1] "2.0 - 369.9 (56.8)" "0.2 - 340.1 (53.2)"
[1] "hr=" "1.4"
D34V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  BRAF MUTATED          7       2      15        3       13        9         4
  BRAF WILD-TYPE        3       4      10        7       12        9         6
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BRAF MUTATED           4         5        23          8         12         17
  BRAF WILD-TYPE        10         5        13          6         14         26
                vv
clus             STAGE IV
  BRAF MUTATED          7
  BRAF WILD-TYPE        9
D34V4, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  I/II NOS              7              3
  STAGE 0               2              4
  STAGE I              15             10
  STAGE IA              3              7
  STAGE IB             13             12
  STAGE II              9              9
  STAGE IIA             4              6
  STAGE IIB             4             10
  STAGE IIC             5              5
  STAGE III            23             13
  STAGE IIIA            8              6
  STAGE IIIB           12             14
  STAGE IIIC           17             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 35 18
  BRAF WILD-TYPE    20 30 25 37
D34V5, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  T0+T1           33             20
  T2              32             30
  T3              35             25
  T4              18             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  BRAF MUTATED   69 33 19 12
  BRAF WILD-TYPE 74 20 15 23
D34V6, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           69             74
  N1           33             20
  N2           19             15
  N3           12             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"
D34V7, binary
                cls
clus               0   1
  BRAF MUTATED   131   8
  BRAF WILD-TYPE 125   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    131    8
  BRAF WILD-TYPE  125    9
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0          131            125
  1            8              9
[1] 2 2
[1] FALSE
D34V8, binary
                cls
clus              0  1
  BRAF MUTATED   51 32
  BRAF WILD-TYPE 56 41
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     51   32
  BRAF WILD-TYPE   56   41
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            51             56
  YES           32             41
[1] 2 2
[1] FALSE
D34V9, binary
                cls
clus               0   1
  BRAF MUTATED    20 125
  BRAF WILD-TYPE  17 128
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     20  125
  BRAF WILD-TYPE   17  128
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            20             17
  YES          125            128
[1] 2 2
[1] FALSE
D34V10, continuous
D34V11, binary
                cls
clus              0  1
  BRAF MUTATED   58 87
  BRAF WILD-TYPE 51 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     58   87
  BRAF WILD-TYPE   51   94
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           58             51
  MALE             87             94
[1] 2 2
[1] FALSE
D34V12, binary
                cls
clus               0   1
  BRAF MUTATED   127  18
  BRAF WILD-TYPE 127  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    127   18
  BRAF WILD-TYPE  127   17
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO           127            127
  YES           18             17
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       1                         0   144
  BRAF WILD-TYPE     4                         1   140
D34V13, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                              144            140
[1] 3 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
  BRAF MUTATED     1 142
  BRAF WILD-TYPE   2 141
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1  142
  BRAF WILD-TYPE    2  141
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO          142            141
[1] 2 2
[1] FALSE

Clustering(35) Variable = NBPF1 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2              0  1
  NBPF1 MUTATED   12  7
  NBPF1 WILD-TYPE 85 96
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             19             181 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              7              96 
$`NBPF1 MUTATED`
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GL 
       52.90        27.35        36.85        76.41        15.75        42.05 
TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2GN 
       76.34        13.15         0.00         0.26        47.41        93.63 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AF TCGA-ER-A19G 
        0.20        81.99       103.13       124.31         6.28       184.60 
TCGA-ER-A19P 
      120.76 

$`NBPF1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
      134.40        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        19.04        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
       30.67       144.46        31.76        62.70        11.34        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
      177.86        15.02        22.29        69.21        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       18.21        24.89        20.38        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P 
       75.22        76.14        12.99        44.28        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       18.35         0.76        71.31        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      145.45       227.01       143.93        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       64.04         4.41        54.51        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H 
        7.82         4.54        53.29        39.81        11.47       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       99.06        59.84        42.51        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
            0.0             0.2 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         184.60          346.49 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          47.41           47.18 
[1] "0.0 - 184.6 (47.4)" "0.2 - 346.5 (47.2)"
[1] "hr=" "1.2"
D35V2, survival
                 sevent
clus2               0   1
  NBPF1 MUTATED    13  12
  NBPF1 WILD-TYPE 111 148
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             25             259 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
             12             148 
$`NBPF1 MUTATED`
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GL 
      126.81        27.35        36.95        90.90       115.53       125.79 
TCGA-DA-A1HV TCGA-DA-A1I4 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29E TCGA-EE-A29H 
       76.57        35.93        29.82        14.70        63.78        64.64 
TCGA-EE-A29S TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A3AA 
       61.28       102.12        42.77        94.82       129.27       124.31 
TCGA-EE-A3AF TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19P TCGA-FS-A1ZA TCGA-FS-A1ZK 
       13.81        26.37       302.07       162.08        27.72        23.93 
TCGA-GF-A6C9 
       15.78 

$`NBPF1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 
       68.15       168.26         2.60       340.14       134.40        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49        23.77       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        66.48        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-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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29         9.90        25.18        77.56        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       222.51       176.55       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       58.92         7.04        36.46        27.22         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M 
       63.35        85.08        78.97        13.97        72.07        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        66.74        14.47       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS 
      107.38        54.74        79.66        75.48        13.91        81.21 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        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 
      180.39       216.66       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        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       48.89        12.59        13.02       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        44.09        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
          13.81            0.20 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
         302.07          369.93 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          63.78           53.52 
[1] "13.8 - 302.1 (63.8)" "0.2 - 369.9 (53.5)" 
[1] "hr=" "1.2"
D35V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  NBPF1 MUTATED          0       1       1        3        2        3         2
  NBPF1 WILD-TYPE       10       5      24        7       23       15         8
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NBPF1 MUTATED           0         0         3          1          4
  NBPF1 WILD-TYPE        14        10        33         13         22
                 vv
clus              STAGE IIIC STAGE IV
  NBPF1 MUTATED            3        0
  NBPF1 WILD-TYPE         40       16
D35V4, multiclass
            clus
vv           NBPF1 MUTATED NBPF1 WILD-TYPE
  I/II NOS               0              10
  STAGE 0                1               5
  STAGE I                1              24
  STAGE IA               3               7
  STAGE IB               2              23
  STAGE II               3              15
  STAGE IIA              2               8
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              3              33
  STAGE IIIA             1              13
  STAGE IIIB             4              22
  STAGE IIIC             3              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
  NBPF1 MUTATED       7  4  4  4
  NBPF1 WILD-TYPE    46 58 56 51
D35V5, multiclass
       clus
vv      NBPF1 MUTATED NBPF1 WILD-TYPE
  T0+T1             7              46
  T2                4              58
  T3                4              56
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NBPF1 MUTATED    15   3   6   1
  NBPF1 WILD-TYPE 128  50  28  34
D35V6, multiclass
    clus
vv   NBPF1 MUTATED NBPF1 WILD-TYPE
  N0            15             128
  N1             3              50
  N2             6              28
  N3             1              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"
D35V7, binary
                 cls
clus                0   1
  NBPF1 MUTATED    25   0
  NBPF1 WILD-TYPE 231  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     25    0
  NBPF1 WILD-TYPE  231   17
   clus
vv  NBPF1 MUTATED NBPF1 WILD-TYPE
  0            25             231
  1             0              17
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus               0  1
  NBPF1 MUTATED   11  4
  NBPF1 WILD-TYPE 96 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     11    4
  NBPF1 WILD-TYPE   96   69
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO             11              96
  YES             4              69
[1] 2 2
[1] FALSE
D35V9, binary
                 cls
clus                0   1
  NBPF1 MUTATED     5  21
  NBPF1 WILD-TYPE  32 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      5   21
  NBPF1 WILD-TYPE   32  232
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO              5              32
  YES            21             232
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, binary
                 cls
clus                0   1
  NBPF1 MUTATED     9  17
  NBPF1 WILD-TYPE 100 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      9   17
  NBPF1 WILD-TYPE  100  164
        clus
vv       NBPF1 MUTATED NBPF1 WILD-TYPE
  FEMALE             9             100
  MALE              17             164
[1] 2 2
[1] FALSE
D35V12, binary
                 cls
clus                0   1
  NBPF1 MUTATED    23   3
  NBPF1 WILD-TYPE 231  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED     23    3
  NBPF1 WILD-TYPE  231   32
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO             23             231
  YES             3              32
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF1 MUTATED       0                         0    26
  NBPF1 WILD-TYPE     5                         1   258
D35V13, multiclass
                           clus
vv                          NBPF1 MUTATED NBPF1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                26             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"
D35V14, binary
                 cls
clus                0   1
  NBPF1 MUTATED     0  25
  NBPF1 WILD-TYPE   3 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      0   25
  NBPF1 WILD-TYPE    3  258
                        clus
vv                       NBPF1 MUTATED NBPF1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            25             258
[1] 2 2
[1] FALSE

Clustering(36) Variable = ZNF780B MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                 0   1
  ZNF780B MUTATED     3   3
  ZNF780B WILD-TYPE  94 100
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                6               194 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                3               100 
$`ZNF780B MUTATED`
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-EE-A29C TCGA-EE-A3AE TCGA-ER-A2NF 
      269.03       134.40        36.85        76.14        54.51        10.19 

$`ZNF780B WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       166.75        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       27.35        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.22        12.99         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       64.04         4.41         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  ZNF780B MUTATED ZNF780B WILD-TYPE 
            10.19              0.00 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           269.03            346.49 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           65.325            47.050 
[1] "10.2 - 269.0 (65.3)" "0.0 - 346.5 (47.0)" 
[1] "hr=" "1.5"
D36V2, survival
                   sevent
clus2                 0   1
  ZNF780B MUTATED     5   5
  ZNF780B WILD-TYPE 119 155
  ZNF780B MUTATED ZNF780B WILD-TYPE 
               10               274 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
                5               155 
$`ZNF780B MUTATED`
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-EE-A29C TCGA-EE-A2GC TCGA-EE-A2MD 
      340.14       134.40        36.95        78.97        67.43        47.28 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-ER-A2NF TCGA-GF-A6C9 
       54.51        41.59        28.83        15.78 

$`ZNF780B WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
       68.15       168.26         2.60       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        85.08        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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-A2GE 
      115.96        59.64        39.29        86.14        59.28       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      216.66       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        64.04        28.77 
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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19       201.80        51.35       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        19.43         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  ZNF780B MUTATED ZNF780B WILD-TYPE 
            15.78              0.20 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           340.14            369.93 
  ZNF780B MUTATED ZNF780B WILD-TYPE 
           50.895            53.970 
[1] "15.8 - 340.1 (50.9)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1.4"
D36V3, continuous
                   vv
clus                I/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      24        9       24       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ZNF780B MUTATED           0         2         0         2          0
  ZNF780B WILD-TYPE        10        12        10        34         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  ZNF780B MUTATED            2          0        0
  ZNF780B WILD-TYPE         24         43       16
D36V4, multiclass
            clus
vv           ZNF780B MUTATED ZNF780B WILD-TYPE
  I/II NOS                 0                10
  STAGE 0                  0                 6
  STAGE I                  1                24
  STAGE IA                 1                 9
  STAGE IB                 1                24
  STAGE II                 1                17
  STAGE IIA                0                10
  STAGE IIB                2                12
  STAGE IIC                0                10
  STAGE III                2                34
  STAGE IIIA               0                14
  STAGE IIIB               2                24
  STAGE IIIC               0                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
  ZNF780B MUTATED       2  2  3  1
  ZNF780B WILD-TYPE    51 60 57 54
D36V5, multiclass
       clus
vv      ZNF780B MUTATED ZNF780B WILD-TYPE
  T0+T1               2                51
  T2                  2                60
  T3                  3                57
  T4                  1                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZNF780B MUTATED     6   0   2   1
  ZNF780B WILD-TYPE 137  53  32  34
D36V6, multiclass
    clus
vv   ZNF780B MUTATED ZNF780B WILD-TYPE
  N0               6               137
  N1               0                53
  N2               2                32
  N3               1                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"
D36V7, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     9   0
  ZNF780B WILD-TYPE 247  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      9    0
  ZNF780B WILD-TYPE  247   17
   clus
vv  ZNF780B MUTATED ZNF780B WILD-TYPE
  0               9               247
  1               0                17
[1] 2 2
[1] FALSE
D36V8, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     3   4
  ZNF780B WILD-TYPE 104  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      3    4
  ZNF780B WILD-TYPE  104   69
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  NO                3               104
  YES               4                69
[1] 2 2
[1] FALSE
D36V9, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     2   8
  ZNF780B WILD-TYPE  35 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      2    8
  ZNF780B WILD-TYPE   35  245
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  NO                2                35
  YES               8               245
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     2   8
  ZNF780B WILD-TYPE 107 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      2    8
  ZNF780B WILD-TYPE  107  173
        clus
vv       ZNF780B MUTATED ZNF780B WILD-TYPE
  FEMALE               2               107
  MALE                 8               173
[1] 2 2
[1] FALSE
D36V12, binary
                   cls
clus                  0   1
  ZNF780B MUTATED     8   2
  ZNF780B WILD-TYPE 246  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      8    2
  ZNF780B WILD-TYPE  246   33
     clus
vv    ZNF780B MUTATED ZNF780B WILD-TYPE
  NO                8               246
  YES               2                33
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF780B MUTATED       0                         0    10
  ZNF780B WILD-TYPE     5                         1   274
D36V13, multiclass
                           clus
vv                          ZNF780B MUTATED ZNF780B WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10               274
[1] 3 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
  ZNF780B MUTATED     0  10
  ZNF780B WILD-TYPE   3 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780B MUTATED      0   10
  ZNF780B WILD-TYPE    3  273
                        clus
vv                       ZNF780B MUTATED ZNF780B WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              10               273
[1] 2 2
[1] FALSE

Clustering(37) Variable = STK19 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2              0  1
  STK19 MUTATED    3  6
  STK19 WILD-TYPE 94 97
  STK19 MUTATED STK19 WILD-TYPE 
              9             191 
  STK19 MUTATED STK19 WILD-TYPE 
              6              97 
$`STK19 MUTATED`
TCGA-EE-A2GD TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A183 
      269.03        22.29        69.21        76.34        20.38        26.24 
TCGA-EE-A2MG TCGA-EE-A3JI TCGA-OD-A75X 
       94.19       135.98       297.01 

$`STK19 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      134.40        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       15.02        22.85       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        0.00        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       15.25         5.75        23.77       209.79       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       19.86        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92         7.23         0.20         0.33 

  STK19 MUTATED STK19 WILD-TYPE 
          20.38            0.00 
  STK19 MUTATED STK19 WILD-TYPE 
         297.01          346.49 
  STK19 MUTATED STK19 WILD-TYPE 
          76.34           46.92 
[1] "20.4 - 297.0 (76.3)" "0.0 - 346.5 (46.9)" 
[1] "hr=" "1.4"
D37V2, survival
                 sevent
clus2               0   1
  STK19 MUTATED     5   9
  STK19 WILD-TYPE 119 151
  STK19 MUTATED STK19 WILD-TYPE 
             14             270 
  STK19 MUTATED STK19 WILD-TYPE 
              9             151 
$`STK19 MUTATED`
TCGA-EE-A2GD TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A183 
      340.14        22.29        77.56        76.57        33.73        26.89 
TCGA-EE-A185 TCGA-EE-A2GI TCGA-EE-A2MG TCGA-EE-A3JI TCGA-FS-A1ZA TCGA-GF-A6C9 
        4.96        48.72       103.20       152.81        27.72        15.78 
TCGA-GN-A266 TCGA-OD-A75X 
       10.13       297.90 

$`STK19 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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-A6E9 
      151.53        54.67         3.65         7.10        15.39         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        22.95        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A20B 
       36.46        29.82        27.22         8.65        14.70       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        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       86.14        59.28        67.43       173.79       220.24       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81        41.59 
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-ER-A195 TCGA-ER-A197 
       53.19       201.80        51.35       134.33        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.43         2.04       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13         7.23         0.20         0.33         0.69 

  STK19 MUTATED STK19 WILD-TYPE 
           4.96            0.20 
  STK19 MUTATED STK19 WILD-TYPE 
         340.14          369.93 
  STK19 MUTATED STK19 WILD-TYPE 
         41.225          54.215 
[1] "5.0 - 340.1 (41.2)" "0.2 - 369.9 (54.2)"
[1] "hr=" "1.1"
D37V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  STK19 MUTATED          0       1       2        1        0        1         0
  STK19 WILD-TYPE       10       5      23        9       25       17        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  STK19 MUTATED           1         0         0          1          4
  STK19 WILD-TYPE        13        10        36         13         22
                 vv
clus              STAGE IIIC STAGE IV
  STK19 MUTATED            1        0
  STK19 WILD-TYPE         42       16
D37V4, multiclass
            clus
vv           STK19 MUTATED STK19 WILD-TYPE
  I/II NOS               0              10
  STAGE 0                1               5
  STAGE I                2              23
  STAGE IA               1               9
  STAGE IB               0              25
  STAGE II               1              17
  STAGE IIA              0              10
  STAGE IIB              1              13
  STAGE IIC              0              10
  STAGE III              0              36
  STAGE IIIA             1              13
  STAGE IIIB             4              22
  STAGE IIIC             1              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
  STK19 MUTATED       2  2  3  3
  STK19 WILD-TYPE    51 60 57 52
D37V5, multiclass
       clus
vv      STK19 MUTATED STK19 WILD-TYPE
  T0+T1             2              51
  T2                2              60
  T3                3              57
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STK19 MUTATED     6   2   2   1
  STK19 WILD-TYPE 137  51  32  34
D37V6, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  N0             6             137
  N1             2              51
  N2             2              32
  N3             1              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"
D37V7, binary
                 cls
clus                0   1
  STK19 MUTATED    12   0
  STK19 WILD-TYPE 244  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED     12    0
  STK19 WILD-TYPE  244   17
   clus
vv  STK19 MUTATED STK19 WILD-TYPE
  0            12             244
  1             0              17
[1] 2 2
[1] FALSE
D37V8, binary
                 cls
clus                0   1
  STK19 MUTATED     4   3
  STK19 WILD-TYPE 103  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      4    3
  STK19 WILD-TYPE  103   70
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              4             103
  YES             3              70
[1] 2 2
[1] FALSE
D37V9, binary
                 cls
clus                0   1
  STK19 MUTATED     3  11
  STK19 WILD-TYPE  34 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      3   11
  STK19 WILD-TYPE   34  242
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              3              34
  YES            11             242
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, binary
                 cls
clus                0   1
  STK19 MUTATED     6   8
  STK19 WILD-TYPE 103 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      6    8
  STK19 WILD-TYPE  103  173
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             6             103
  MALE               8             173
[1] 2 2
[1] FALSE
D37V12, binary
                 cls
clus                0   1
  STK19 MUTATED    11   3
  STK19 WILD-TYPE 243  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED     11    3
  STK19 WILD-TYPE  243   32
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO             11             243
  YES             3              32
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK19 MUTATED       0                         0    14
  STK19 WILD-TYPE     5                         1   270
D37V13, multiclass
                           clus
vv                          STK19 MUTATED STK19 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                14             270
[1] 3 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
  STK19 MUTATED     0  14
  STK19 WILD-TYPE   3 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0   14
  STK19 WILD-TYPE    3  269
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            14             269
[1] 2 2
[1] FALSE

Clustering(38) Variable = KYNU MUTATION ANALYSIS
D38V1, survival
                sevent
clus2             0  1
  KYNU MUTATED   11  5
  KYNU WILD-TYPE 86 98
  KYNU MUTATED KYNU WILD-TYPE 
            16            184 
  KYNU MUTATED KYNU WILD-TYPE 
             5             98 
$`KYNU MUTATED`
TCGA-EE-A20H TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A1Q8 TCGA-D3-A2JP TCGA-D3-A51R 
      166.75       134.40        36.85        19.04        43.53        62.70 
TCGA-DA-A1HV TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2MI TCGA-EE-A3JB TCGA-EE-A3JI 
       76.34         0.26        77.98       171.85       168.85       135.98 
TCGA-FS-A1ZM TCGA-FS-A1ZZ TCGA-GF-A6C8 TCGA-GN-A4U3 
       78.61         3.06         1.91       120.53 

$`KYNU WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       27.35        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        64.83        66.08        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       144.46        31.76        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
      177.86        15.02        22.29        69.21        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       75.55        79.20        75.22        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        30.02        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       45.90         3.35        19.86        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 
       11.54        19.30         9.90        18.25        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 
       96.92        17.06        42.48         7.59        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  KYNU MUTATED KYNU WILD-TYPE 
          0.26           0.00 
  KYNU MUTATED KYNU WILD-TYPE 
        171.85         346.49 
  KYNU MUTATED KYNU WILD-TYPE 
        77.160         46.455 
[1] "0.3 - 171.8 (77.2)" "0.0 - 346.5 (46.5)"
[1] "hr=" "2"  
D38V2, survival
                sevent
clus2              0   1
  KYNU MUTATED    11   5
  KYNU WILD-TYPE 113 155
  KYNU MUTATED KYNU WILD-TYPE 
            16            268 
  KYNU MUTATED KYNU WILD-TYPE 
             5            155 
$`KYNU MUTATED`
TCGA-EE-A20H TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A1Q8 TCGA-D3-A2JP TCGA-D3-A51R 
      168.26       134.40        36.95        28.08        59.57        63.81 
TCGA-DA-A1HV TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2MI TCGA-EE-A3JB TCGA-EE-A3JI 
       76.57        63.78        86.14       204.66       201.80       152.81 
TCGA-FS-A1ZM TCGA-FS-A1ZZ TCGA-GF-A6C8 TCGA-GN-A4U3 
      101.26        27.02         2.04       121.91 

$`KYNU WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
       68.15         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08       130.72        58.06        46.98       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-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29         9.90        25.18        77.56        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
       17.92        46.82       115.96        59.64        39.29        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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 
       64.04        28.77        54.51        13.81        41.59       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       134.33        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A262 
       13.51        19.30         9.90        19.43        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       48.00        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  KYNU MUTATED KYNU WILD-TYPE 
          2.04           0.20 
  KYNU MUTATED KYNU WILD-TYPE 
        204.66         369.93 
  KYNU MUTATED KYNU WILD-TYPE 
        81.355         53.175 
[1] "2.0 - 204.7 (81.4)" "0.2 - 369.9 (53.2)"
[1] "hr=" "2.3"
D38V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KYNU MUTATED          0       0       3        1        0        0         1
  KYNU WILD-TYPE       10       6      22        9       25       18         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KYNU MUTATED           3         0         4          0          2          1
  KYNU WILD-TYPE        11        10        32         14         24         42
                vv
clus             STAGE IV
  KYNU MUTATED          1
  KYNU WILD-TYPE       15
D38V4, multiclass
            clus
vv           KYNU MUTATED KYNU WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               3             22
  STAGE IA              1              9
  STAGE IB              0             25
  STAGE II              0             18
  STAGE IIA             1              9
  STAGE IIB             3             11
  STAGE IIC             0             10
  STAGE III             4             32
  STAGE IIIA            0             14
  STAGE IIIB            2             24
  STAGE IIIC            1             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
  KYNU MUTATED       4  4  6  1
  KYNU WILD-TYPE    49 58 54 54
D38V5, multiclass
       clus
vv      KYNU MUTATED KYNU WILD-TYPE
  T0+T1            4             49
  T2               4             58
  T3               6             54
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KYNU MUTATED     7   3   3   2
  KYNU WILD-TYPE 136  50  31  33
D38V6, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  N0            7            136
  N1            3             50
  N2            3             31
  N3            2             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"
D38V7, binary
                cls
clus               0   1
  KYNU MUTATED    15   1
  KYNU WILD-TYPE 241  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED     15    1
  KYNU WILD-TYPE  241   16
   clus
vv  KYNU MUTATED KYNU WILD-TYPE
  0           15            241
  1            1             16
[1] 2 2
[1] FALSE
D38V8, binary
                cls
clus               0   1
  KYNU MUTATED     6   2
  KYNU WILD-TYPE 101  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      6    2
  KYNU WILD-TYPE  101   71
     clus
vv    KYNU MUTATED KYNU WILD-TYPE
  NO             6            101
  YES            2             71
[1] 2 2
[1] FALSE
D38V9, binary
                cls
clus               0   1
  KYNU MUTATED     3  13
  KYNU WILD-TYPE  34 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      3   13
  KYNU WILD-TYPE   34  240
     clus
vv    KYNU MUTATED KYNU WILD-TYPE
  NO             3             34
  YES           13            240
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, binary
                cls
clus               0   1
  KYNU MUTATED     4  12
  KYNU WILD-TYPE 105 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      4   12
  KYNU WILD-TYPE  105  169
        clus
vv       KYNU MUTATED KYNU WILD-TYPE
  FEMALE            4            105
  MALE             12            169
[1] 2 2
[1] FALSE
D38V12, binary
                cls
clus               0   1
  KYNU MUTATED    11   5
  KYNU WILD-TYPE 243  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED     11    5
  KYNU WILD-TYPE  243   30
     clus
vv    KYNU MUTATED KYNU WILD-TYPE
  NO            11            243
  YES            5             30
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KYNU MUTATED       0                         0    16
  KYNU WILD-TYPE     5                         1   268
D38V13, multiclass
                           clus
vv                          KYNU MUTATED KYNU WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               16            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"
D38V14, binary
                cls
clus               0   1
  KYNU MUTATED     1  15
  KYNU WILD-TYPE   2 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      1   15
  KYNU WILD-TYPE    2  268
                        clus
vv                       KYNU MUTATED KYNU WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           15            268
[1] 2 2
[1] FALSE

Clustering(39) Variable = ANO4 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2             0  1
  ANO4 MUTATED   16 17
  ANO4 WILD-TYPE 81 86
  ANO4 MUTATED ANO4 WILD-TYPE 
            33            167 
  ANO4 MUTATED ANO4 WILD-TYPE 
            17             86 
$`ANO4 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q4 TCGA-D3-A2J7 
       62.07       134.40        27.35        36.85        31.89        45.99 
TCGA-D3-A3MR TCGA-D3-A51R TCGA-DA-A1HY TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17X 
       90.21        62.70       138.67        58.85       225.11        13.15 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29Q 
       20.38        75.55        12.99         0.26        47.74        61.12 
TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MS TCGA-EE-A3AC 
      201.60         0.20       209.79       104.78       143.93        64.04 
TCGA-EE-A3AE TCGA-ER-A195 TCGA-ER-A19P TCGA-ER-A42L TCGA-FS-A1ZD TCGA-FS-A1ZZ 
       54.51        34.45       120.76        74.47        32.78         3.06 
TCGA-FW-A3TU TCGA-GN-A4U4 TCGA-QB-A6FS 
       55.59        34.49         7.23 

$`ANO4 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       19.04         8.42        15.72       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        76.41        62.60        25.64        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       31.76        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.29        69.21        22.85        76.34        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q 
      110.53        60.10        64.83        30.44        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       16.41        52.41        18.21        24.89         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       79.20        75.22        76.14        44.28        47.41        27.16 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       23.77        94.19       171.85        63.25        89.26       145.45 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      227.01        23.51        53.26       124.31       122.73         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       19.86       135.98        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       15.48        32.05         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98         8.35        27.62       312.07        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       23.21         5.29        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       80.68        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
      120.53        46.92       297.01         0.20         0.33 

  ANO4 MUTATED ANO4 WILD-TYPE 
           0.2            0.0 
  ANO4 MUTATED ANO4 WILD-TYPE 
        225.11         346.49 
  ANO4 MUTATED ANO4 WILD-TYPE 
         55.59          45.90 
[1] "0.2 - 225.1 (55.6)" "0.0 - 346.5 (45.9)"
[1] "hr=" "1"  
D39V2, survival
                sevent
clus2              0   1
  ANO4 MUTATED    19  26
  ANO4 WILD-TYPE 105 134
  ANO4 MUTATED ANO4 WILD-TYPE 
            45            239 
  ANO4 MUTATED ANO4 WILD-TYPE 
            26            134 
$`ANO4 MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EE-A29L TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 
       62.07        13.87         2.60       134.40        27.35        36.95 
TCGA-D3-A1Q4 TCGA-D3-A2J7 TCGA-D3-A3MR TCGA-D3-A51R TCGA-DA-A1HY TCGA-DA-A1I8 
      112.04       103.10       103.59        63.81       144.89        53.92 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29D 
       68.09       225.96        29.82        33.73       151.27        13.97 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2GH 
       63.78        56.84        18.61        66.74        61.28       220.24 
TCGA-EE-A2GI TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MS 
       48.72        42.77        21.67       268.73       216.66       162.48 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-ER-A195 TCGA-ER-A19P 
       64.04        54.51        41.59        36.95        35.44       162.08 
TCGA-ER-A42L TCGA-FS-A1ZD TCGA-FS-A1ZZ TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C9 
      149.03        53.52        27.02        26.73        55.59        15.78 
TCGA-GN-A4U4 TCGA-QB-A6FS TCGA-RP-A694 
       39.35         7.23         0.69 

$`ANO4 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20H 
       46.32        68.25        54.02        94.98        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 
      340.14       126.81        31.40        50.76        15.45        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74        43.43        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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         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-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        26.89       125.79       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 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
       35.93       135.02        88.87        65.92        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       10.49        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
       58.92         7.04        36.46        27.22         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       133.81        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29R 
       85.08        78.97        72.07        64.64        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       81.21        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       180.39       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21        53.26       124.31       122.73        28.77        13.81 
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-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
      201.80        51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        33.21        12.95        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        46.45 
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        34.03 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       54.41        80.68        17.46        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       19.43         2.04       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 
       64.44        62.79        32.48        48.00       121.91        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         0.20         0.33 

  ANO4 MUTATED ANO4 WILD-TYPE 
          0.69           0.20 
  ANO4 MUTATED ANO4 WILD-TYPE 
        268.73         369.93 
  ANO4 MUTATED ANO4 WILD-TYPE 
         54.51          53.26 
[1] "0.7 - 268.7 (54.5)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1"  
D39V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ANO4 MUTATED          2       1       5        4        1        5         4
  ANO4 WILD-TYPE        8       5      20        6       24       13         6
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ANO4 MUTATED           2         1         8          1          3          5
  ANO4 WILD-TYPE        12         9        28         13         23         38
                vv
clus             STAGE IV
  ANO4 MUTATED          1
  ANO4 WILD-TYPE       15
D39V4, multiclass
            clus
vv           ANO4 MUTATED ANO4 WILD-TYPE
  I/II NOS              2              8
  STAGE 0               1              5
  STAGE I               5             20
  STAGE IA              4              6
  STAGE IB              1             24
  STAGE II              5             13
  STAGE IIA             4              6
  STAGE IIB             2             12
  STAGE IIC             1              9
  STAGE III             8             28
  STAGE IIIA            1             13
  STAGE IIIB            3             23
  STAGE IIIC            5             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 11 13  4
  ANO4 WILD-TYPE    44 51 47 51
D39V5, multiclass
       clus
vv      ANO4 MUTATED ANO4 WILD-TYPE
  T0+T1            9             44
  T2              11             51
  T3              13             47
  T4               4             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ANO4 MUTATED    26   8   6   2
  ANO4 WILD-TYPE 117  45  28  33
D39V6, multiclass
    clus
vv   ANO4 MUTATED ANO4 WILD-TYPE
  N0           26            117
  N1            8             45
  N2            6             28
  N3            2             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"
D39V7, binary
                cls
clus               0   1
  ANO4 MUTATED    43   1
  ANO4 WILD-TYPE 213  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     43    1
  ANO4 WILD-TYPE  213   16
   clus
vv  ANO4 MUTATED ANO4 WILD-TYPE
  0           43            213
  1            1             16
[1] 2 2
[1] FALSE
D39V8, binary
                cls
clus              0  1
  ANO4 MUTATED   16 10
  ANO4 WILD-TYPE 91 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     16   10
  ANO4 WILD-TYPE   91   63
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  NO            16             91
  YES           10             63
[1] 2 2
[1] FALSE
D39V9, binary
                cls
clus               0   1
  ANO4 MUTATED     7  39
  ANO4 WILD-TYPE  30 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED      7   39
  ANO4 WILD-TYPE   30  214
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  NO             7             30
  YES           39            214
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, binary
                cls
clus               0   1
  ANO4 MUTATED    12  34
  ANO4 WILD-TYPE  97 147
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     12   34
  ANO4 WILD-TYPE   97  147
        clus
vv       ANO4 MUTATED ANO4 WILD-TYPE
  FEMALE           12             97
  MALE             34            147
[1] 2 2
[1] FALSE
D39V12, binary
                cls
clus               0   1
  ANO4 MUTATED    43   3
  ANO4 WILD-TYPE 211  32
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED     43    3
  ANO4 WILD-TYPE  211   32
     clus
vv    ANO4 MUTATED ANO4 WILD-TYPE
  NO            43            211
  YES            3             32
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANO4 MUTATED       0                         0    46
  ANO4 WILD-TYPE     5                         1   238
D39V13, multiclass
                           clus
vv                          ANO4 MUTATED ANO4 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               46            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"
D39V14, binary
                cls
clus               0   1
  ANO4 MUTATED     1  44
  ANO4 WILD-TYPE   2 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANO4 MUTATED      1   44
  ANO4 WILD-TYPE    2  239
                        clus
vv                       ANO4 MUTATED ANO4 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           44            239
[1] 2 2
[1] FALSE

Clustering(40) Variable = SLC27A5 MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  SLC27A5 MUTATED     4   2
  SLC27A5 WILD-TYPE  93 101
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                6               194 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                2               101 
$`SLC27A5 MUTATED`
TCGA-D3-A51T TCGA-EE-A17X TCGA-EE-A3AC TCGA-EE-A3JI TCGA-ER-A42L TCGA-GN-A4U4 
       11.34        13.15        64.04       135.98        74.47        34.49 

$`SLC27A5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        31.76        62.70        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 
      111.85        45.90         3.35       168.85        19.86        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       32.05         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       42.48         7.59       120.53        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
            11.34              0.00 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           135.98            346.49 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           49.265            47.295 
[1] "11.3 - 136.0 (49.3)" "0.0 - 346.5 (47.3)" 
[1] "hr=" "1.3"
D40V2, survival
                   sevent
clus2                 0   1
  SLC27A5 MUTATED     5   5
  SLC27A5 WILD-TYPE 119 155
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
               10               274 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
                5               155 
$`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        64.04        41.59 
TCGA-EE-A3JI TCGA-ER-A42L TCGA-FS-A4FC TCGA-GN-A4U4 
      152.81       149.03        54.41        39.35 

$`SLC27A5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        58.06       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-A5GL 
       56.35       145.12        32.94        22.62        63.81       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       58.92         7.04        36.46        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        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-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      134.33        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21        12.95        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        46.45 
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-A3TU TCGA-FW-A3TV 
       34.03        26.73        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       48.00       121.91        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
            26.89              0.20 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           152.81            369.93 
  SLC27A5 MUTATED SLC27A5 WILD-TYPE 
           47.130            54.265 
[1] "26.9 - 152.8 (47.1)" "0.2 - 369.9 (54.3)" 
[1] "hr=" "1"  
D40V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SLC27A5 MUTATED          0       0       1        1        0        2
  SLC27A5 WILD-TYPE       10       6      24        9       25       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SLC27A5 MUTATED           2         0         0         3          0
  SLC27A5 WILD-TYPE         8        14        10        33         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC27A5 MUTATED            0          1        0
  SLC27A5 WILD-TYPE         26         42       16
D40V4, multiclass
            clus
vv           SLC27A5 MUTATED SLC27A5 WILD-TYPE
  I/II NOS                 0                10
  STAGE 0                  0                 6
  STAGE I                  1                24
  STAGE IA                 1                 9
  STAGE IB                 0                25
  STAGE II                 2                16
  STAGE IIA                2                 8
  STAGE IIB                0                14
  STAGE IIC                0                10
  STAGE III                3                33
  STAGE IIIA               0                14
  STAGE IIIB               0                26
  STAGE IIIC               1                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
  SLC27A5 MUTATED       4  2  3  1
  SLC27A5 WILD-TYPE    49 60 57 54
D40V5, multiclass
       clus
vv      SLC27A5 MUTATED SLC27A5 WILD-TYPE
  T0+T1               4                49
  T2                  2                60
  T3                  3                57
  T4                  1                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC27A5 MUTATED     5   2   2   0
  SLC27A5 WILD-TYPE 138  51  32  35
D40V6, multiclass
    clus
vv   SLC27A5 MUTATED SLC27A5 WILD-TYPE
  N0               5               138
  N1               2                51
  N2               2                32
  N3               0                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"
D40V7, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED    10   0
  SLC27A5 WILD-TYPE 246  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED     10    0
  SLC27A5 WILD-TYPE  246   17
   clus
vv  SLC27A5 MUTATED SLC27A5 WILD-TYPE
  0              10               246
  1               0                17
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     4   3
  SLC27A5 WILD-TYPE 103  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      4    3
  SLC27A5 WILD-TYPE  103   70
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  NO                4               103
  YES               3                70
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     3   7
  SLC27A5 WILD-TYPE  34 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    7
  SLC27A5 WILD-TYPE   34  246
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  NO                3                34
  YES               7               246
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     3   7
  SLC27A5 WILD-TYPE 106 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      3    7
  SLC27A5 WILD-TYPE  106  174
        clus
vv       SLC27A5 MUTATED SLC27A5 WILD-TYPE
  FEMALE               3               106
  MALE                 7               174
[1] 2 2
[1] FALSE
D40V12, binary
                   cls
clus                  0   1
  SLC27A5 MUTATED     8   2
  SLC27A5 WILD-TYPE 246  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      8    2
  SLC27A5 WILD-TYPE  246   33
     clus
vv    SLC27A5 MUTATED SLC27A5 WILD-TYPE
  NO                8               246
  YES               2                33
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC27A5 MUTATED       0                         0    10
  SLC27A5 WILD-TYPE     5                         1   274
D40V13, multiclass
                           clus
vv                          SLC27A5 MUTATED SLC27A5 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10               274
[1] 3 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
  SLC27A5 MUTATED     0   9
  SLC27A5 WILD-TYPE   3 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A5 MUTATED      0    9
  SLC27A5 WILD-TYPE    3  274
                        clus
vv                       SLC27A5 MUTATED SLC27A5 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               9               274
[1] 2 2
[1] FALSE

Clustering(41) Variable = POTEG MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2              0  1
  POTEG MUTATED    7  8
  POTEG WILD-TYPE 90 95
  POTEG MUTATED POTEG WILD-TYPE 
             15             185 
  POTEG MUTATED POTEG WILD-TYPE 
              8              95 
$`POTEG MUTATED`
TCGA-EE-A20H TCGA-FW-A3R5 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A182 TCGA-EE-A20C 
      166.75        36.85        76.34       138.67         0.00        75.55 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2MJ TCGA-EE-A3AB TCGA-EE-A3J4 TCGA-EE-A3J7 
       12.99        47.74        63.25       122.73       111.85        45.90 
TCGA-ER-A19D TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.47         3.06        18.51 

$`POTEG WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
      134.40        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.29        69.21        22.85        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       20.38        26.24        79.20        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19       171.85        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J8 
       64.04         4.41        54.51         6.28        67.89         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        39.81       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  POTEG MUTATED POTEG WILD-TYPE 
            0.0             0.2 
  POTEG MUTATED POTEG WILD-TYPE 
         166.75          346.49 
  POTEG MUTATED POTEG WILD-TYPE 
          47.74           47.18 
[1] "0.0 - 166.8 (47.7)" "0.2 - 346.5 (47.2)"
[1] "hr=" "1.2"
D41V2, survival
                 sevent
clus2               0   1
  POTEG MUTATED    10  16
  POTEG WILD-TYPE 114 144
  POTEG MUTATED POTEG WILD-TYPE 
             26             258 
  POTEG MUTATED POTEG WILD-TYPE 
             16             144 
$`POTEG MUTATED`
TCGA-EE-A20H TCGA-EE-A29L TCGA-FW-A3R5 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HY 
      168.26         2.60        36.95         9.90        76.57       144.89 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29V 
       14.70       151.27        13.97        56.84        61.28        25.87 
TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2MJ TCGA-EE-A3AB TCGA-EE-A3AH TCGA-EE-A3J4 
       39.29        48.72        96.23       122.73       138.81       127.20 
TCGA-EE-A3J7 TCGA-ER-A19D TCGA-ER-A19J TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FS-A4F0 
       64.08        12.59         6.44        74.73        27.02        77.82 
TCGA-FS-A4FC TCGA-RP-A694 
       54.41         0.69 

$`POTEG WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       68.15       340.14       126.81       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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-A6EA TCGA-D9-A6EC 
        3.65         7.10        15.39        22.29        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        36.03        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        33.73        26.89         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56        13.55        63.35        85.08        78.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        18.61        56.42        66.74        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      369.93       195.02        17.92        46.82       115.96        59.64 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       86.14        59.28        67.43       173.79       220.24       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       180.39       216.66       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-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       64.04        28.77        54.51        13.81        41.59       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        34.32        53.19       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       48.89        13.02        26.37       302.07       152.35       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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-A4F4 
      148.80        53.16        26.56        49.48        27.09        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73       174.84        34.03        26.73        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 

  POTEG MUTATED POTEG WILD-TYPE 
           0.69            0.20 
  POTEG MUTATED POTEG WILD-TYPE 
         168.26          369.93 
  POTEG MUTATED POTEG WILD-TYPE 
         55.625          53.720 
[1] "0.7 - 168.3 (55.6)" "0.2 - 369.9 (53.7)"
[1] "hr=" "1.3"
D41V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  POTEG MUTATED          0       1       2        1        3        3         2
  POTEG WILD-TYPE       10       5      23        9       22       15         8
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  POTEG MUTATED           2         0         4          1          1
  POTEG WILD-TYPE        12        10        32         13         25
                 vv
clus              STAGE IIIC STAGE IV
  POTEG MUTATED            4        3
  POTEG WILD-TYPE         39       13
D41V4, multiclass
            clus
vv           POTEG MUTATED POTEG WILD-TYPE
  I/II NOS               0              10
  STAGE 0                1               5
  STAGE I                2              23
  STAGE IA               1               9
  STAGE IB               3              22
  STAGE II               3              15
  STAGE IIA              2               8
  STAGE IIB              2              12
  STAGE IIC              0              10
  STAGE III              4              32
  STAGE IIIA             1              13
  STAGE IIIB             1              25
  STAGE IIIC             4              39
  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       3  6  9  4
  POTEG WILD-TYPE    50 56 51 51
D41V5, multiclass
       clus
vv      POTEG MUTATED POTEG WILD-TYPE
  T0+T1             3              50
  T2                6              56
  T3                9              51
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  POTEG MUTATED    15   5   3   2
  POTEG WILD-TYPE 128  48  31  33
D41V6, multiclass
    clus
vv   POTEG MUTATED POTEG WILD-TYPE
  N0            15             128
  N1             5              48
  N2             3              31
  N3             2              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"
D41V7, binary
                 cls
clus                0   1
  POTEG MUTATED    24   3
  POTEG WILD-TYPE 232  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED     24    3
  POTEG WILD-TYPE  232   14
   clus
vv  POTEG MUTATED POTEG WILD-TYPE
  0            24             232
  1             3              14
[1] 2 2
[1] FALSE
D41V8, binary
                 cls
clus               0  1
  POTEG MUTATED   10  8
  POTEG WILD-TYPE 97 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED     10    8
  POTEG WILD-TYPE   97   65
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  NO             10              97
  YES             8              65
[1] 2 2
[1] FALSE
D41V9, binary
                 cls
clus                0   1
  POTEG MUTATED     4  23
  POTEG WILD-TYPE  33 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      4   23
  POTEG WILD-TYPE   33  230
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  NO              4              33
  YES            23             230
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, binary
                 cls
clus                0   1
  POTEG MUTATED     8  19
  POTEG WILD-TYPE 101 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      8   19
  POTEG WILD-TYPE  101  162
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  FEMALE             8             101
  MALE              19             162
[1] 2 2
[1] FALSE
D41V12, binary
                 cls
clus                0   1
  POTEG MUTATED    25   2
  POTEG WILD-TYPE 229  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED     25    2
  POTEG WILD-TYPE  229   33
     clus
vv    POTEG MUTATED POTEG WILD-TYPE
  NO             25             229
  YES             2              33
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POTEG MUTATED       0                         0    27
  POTEG WILD-TYPE     5                         1   257
D41V13, multiclass
                           clus
vv                          POTEG MUTATED POTEG WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                27             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"
D41V14, binary
                 cls
clus                0   1
  POTEG MUTATED     1  26
  POTEG WILD-TYPE   2 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      1   26
  POTEG WILD-TYPE    2  257
                        clus
vv                       POTEG MUTATED POTEG WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            26             257
[1] 2 2
[1] FALSE

Clustering(42) Variable = TPTE MUTATION ANALYSIS
D42V1, survival
                sevent
clus2             0  1
  TPTE MUTATED   20 23
  TPTE WILD-TYPE 77 80
  TPTE MUTATED TPTE WILD-TYPE 
            43            157 
  TPTE MUTATED TPTE WILD-TYPE 
            23             80 
$`TPTE MUTATED`
TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JN 
       52.90        19.04        36.85        15.72       110.93        64.83 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
       11.34        42.05        45.70        69.21        76.34       138.67 
TCGA-DA-A1I1 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29P 
       68.68        20.38         0.00        76.14        12.99        27.16 
TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MF 
       68.65         0.76         0.20       103.13        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       94.19        63.25       104.78       227.01       143.93        23.51 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-ER-A199 TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FS-A1Z3 
       54.51         6.28         7.82        22.36        32.05         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
      312.07        23.21         3.06        55.59         1.91        53.29 
TCGA-GN-A4U3 
      120.53 

$`TPTE WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
      134.40        27.35         8.42        31.89        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      144.46        31.76        62.70       177.86        15.02        22.29 
TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       22.85       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       18.21        13.15        24.89        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       75.22         0.26        44.28        47.41        47.74        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95       201.60        10.62        32.48        18.35        93.63 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MI TCGA-EE-A2MK 
       71.31        81.99        15.25         5.75       171.85        89.26 
TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      145.45        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
      135.98        34.45        10.49         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      120.76        49.71        47.18       146.63        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.62        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
      130.95       136.27        35.28         4.47         5.29        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       66.67       173.19        13.28        80.68        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        9.90        18.25       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
        7.59        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  TPTE MUTATED TPTE WILD-TYPE 
           0.0            0.2 
  TPTE MUTATED TPTE WILD-TYPE 
        312.07         346.49 
  TPTE MUTATED TPTE WILD-TYPE 
         45.70          47.41 
[1] "0.0 - 312.1 (45.7)" "0.2 - 346.5 (47.4)"
[1] "hr=" "1.1"
D42V2, survival
                sevent
clus2              0   1
  TPTE MUTATED    25  39
  TPTE WILD-TYPE  99 121
  TPTE MUTATED TPTE WILD-TYPE 
            64            220 
  TPTE MUTATED TPTE WILD-TYPE 
            39            121 
$`TPTE MUTATED`
TCGA-EE-A29L TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
        2.60       126.81        31.40        36.95        16.67       112.57 
TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3MV TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       66.48        46.98        45.30        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
      137.92         3.65        77.56        76.57        36.03       144.89 
TCGA-DA-A1I1 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
      222.51        33.73        14.70        63.35        78.97        13.97 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GJ TCGA-EE-A2GP 
       18.61        56.42        17.92        46.82       107.38        13.91 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF 
       42.77        21.67       129.27        61.51        47.28       268.73 
TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      103.20        96.23       216.66       248.65       162.48        71.21 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A2NC 
       54.51        13.81        36.95        53.19         9.17        43.82 
TCGA-ER-A3PL TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZP TCGA-FS-A1ZW 
       33.21        20.91        27.72       357.37        74.73        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3TU TCGA-GF-A6C8 
       27.02        28.73        26.73        54.41        55.59         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U3 
       15.78       139.89        10.13       121.91 

$`TPTE WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 
       68.15       168.26       340.14       134.40        27.35        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.45        16.57       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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       166.52        86.93        60.23        24.53         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-A51R TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.94        22.62        63.81       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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       25.18        22.95        20.38       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        8.65        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       13.55        85.08        63.78        72.07        64.64        56.84 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        25.87       195.02 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24        48.72        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
      102.12        81.21        44.88        94.82        28.83        19.76 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
      103.27        16.96       204.66       180.39       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       43.23        53.26       124.31       122.73        64.04        28.77 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        12.95       149.03        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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.79        48.85        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       53.16        26.56        27.09        77.82        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       34.03        80.68        17.46        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       19.43       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       48.00        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  TPTE MUTATED TPTE WILD-TYPE 
          2.04           0.20 
  TPTE MUTATED TPTE WILD-TYPE 
        357.37         369.93 
  TPTE MUTATED TPTE WILD-TYPE 
        48.380         54.705 
[1] "2.0 - 357.4 (48.4)" "0.2 - 369.9 (54.7)"
[1] "hr=" "1.1"
D42V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  TPTE MUTATED          3       0       7        2        7        8         2
  TPTE WILD-TYPE        7       6      18        8       18       10         8
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TPTE MUTATED           3         2         9          2          7          6
  TPTE WILD-TYPE        11         8        27         12         19         37
                vv
clus             STAGE IV
  TPTE MUTATED          2
  TPTE WILD-TYPE       14
D42V4, multiclass
            clus
vv           TPTE MUTATED TPTE WILD-TYPE
  I/II NOS              3              7
  STAGE 0               0              6
  STAGE I               7             18
  STAGE IA              2              8
  STAGE IB              7             18
  STAGE II              8             10
  STAGE IIA             2              8
  STAGE IIB             3             11
  STAGE IIC             2              8
  STAGE III             9             27
  STAGE IIIA            2             12
  STAGE IIIB            7             19
  STAGE IIIC            6             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
  TPTE MUTATED      11 16 16 12
  TPTE WILD-TYPE    42 46 44 43
D42V5, multiclass
       clus
vv      TPTE MUTATED TPTE WILD-TYPE
  T0+T1           11             42
  T2              16             46
  T3              16             44
  T4              12             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TPTE MUTATED    36  14   6   3
  TPTE WILD-TYPE 107  39  28  32
D42V6, multiclass
    clus
vv   TPTE MUTATED TPTE WILD-TYPE
  N0           36            107
  N1           14             39
  N2            6             28
  N3            3             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"
D42V7, binary
                cls
clus               0   1
  TPTE MUTATED    58   2
  TPTE WILD-TYPE 198  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     58    2
  TPTE WILD-TYPE  198   15
   clus
vv  TPTE MUTATED TPTE WILD-TYPE
  0           58            198
  1            2             15
[1] 2 2
[1] FALSE
D42V8, binary
                cls
clus              0  1
  TPTE MUTATED   25 16
  TPTE WILD-TYPE 82 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     25   16
  TPTE WILD-TYPE   82   57
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO            25             82
  YES           16             57
[1] 2 2
[1] FALSE
D42V9, binary
                cls
clus               0   1
  TPTE MUTATED     8  56
  TPTE WILD-TYPE  29 197
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      8   56
  TPTE WILD-TYPE   29  197
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO             8             29
  YES           56            197
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, binary
                cls
clus               0   1
  TPTE MUTATED    27  37
  TPTE WILD-TYPE  82 144
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     27   37
  TPTE WILD-TYPE   82  144
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  FEMALE           27             82
  MALE             37            144
[1] 2 2
[1] FALSE
D42V12, binary
                cls
clus               0   1
  TPTE MUTATED    55   9
  TPTE WILD-TYPE 199  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED     55    9
  TPTE WILD-TYPE  199   26
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO            55            199
  YES            9             26
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE MUTATED       0                         0    64
  TPTE WILD-TYPE     5                         1   220
D42V13, multiclass
                           clus
vv                          TPTE MUTATED TPTE WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               64            220
[1] 3 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
  TPTE MUTATED     1  62
  TPTE WILD-TYPE   2 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      1   62
  TPTE WILD-TYPE    2  221
                        clus
vv                       TPTE MUTATED TPTE WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           62            221
[1] 2 2
[1] FALSE

Clustering(43) Variable = USH2A MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2              0  1
  USH2A MUTATED   32 27
  USH2A WILD-TYPE 65 76
  USH2A MUTATED USH2A WILD-TYPE 
             59             141 
  USH2A MUTATED USH2A WILD-TYPE 
             27              76 
$`USH2A MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2JH 
       52.90       134.40        27.35        19.04        36.85        36.30 
TCGA-D3-A2JP TCGA-D3-A3MR TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GL TCGA-D9-A6EC 
       43.53        90.21       144.46        11.34        42.05        69.21 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A182 
       76.34       138.67        58.85        42.64        20.38         0.00 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
       75.55        76.14        12.99         0.26        47.74        27.16 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU 
      115.43        77.98        68.65        18.35         0.20        81.99 
TCGA-EE-A2M8 TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS 
        5.75       171.85        63.25       104.78       145.45       143.93 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
      124.31       122.73        64.04         4.41         6.28       111.85 
TCGA-EE-A3J8 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3PL 
        3.35         7.82        39.81        47.18        22.36        32.05 
TCGA-FR-A44A TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A1ZZ 
      174.21         8.35       312.07        78.61        23.21         3.06 
TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A3OT TCGA-QB-A6FS 
       18.51        80.68        55.59         9.90         7.23 

$`USH2A WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN 
       15.75       168.00        86.30       107.61       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       66.08        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R 
        9.34        23.67       173.85        30.67        31.76        62.70 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1I1 
       45.70       177.86        15.02        22.29        22.85        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61       110.53        60.10        64.83        30.44       225.11 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q 
       26.24        79.20        75.22        44.28        47.41        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      346.49       185.19        30.02        26.14        12.95       201.60 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       10.62        32.48        93.63         0.76        71.31       103.13 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
       15.25        23.77       209.79        94.19        89.26       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
       23.51        53.26        54.51        67.89        45.90       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       19.86       135.98        34.45        10.49         4.54        53.29 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
      120.76        49.71       146.63        73.05         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42L 
       10.19        28.67       173.29        68.52        15.48        74.47 
TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZD 
        4.50       171.78        49.74       195.98        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       43.92         7.82        36.33       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TV 
        4.47         5.29        66.67       173.19        13.28        11.54 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.30        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
      297.01         0.20         0.33 

  USH2A MUTATED USH2A WILD-TYPE 
            0.0             0.2 
  USH2A MUTATED USH2A WILD-TYPE 
         312.07          346.49 
  USH2A MUTATED USH2A WILD-TYPE 
          47.18           47.41 
[1] "0.0 - 312.1 (47.2)" "0.2 - 346.5 (47.4)"
[1] "hr=" "1"  
D43V2, survival
                 sevent
clus2               0   1
  USH2A MUTATED    39  48
  USH2A WILD-TYPE  85 112
  USH2A MUTATED USH2A WILD-TYPE 
             87             197 
  USH2A MUTATED USH2A WILD-TYPE 
             48             112 
$`USH2A MUTATED`
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
        2.60       126.81       134.40        27.35        31.40        50.76 
TCGA-FW-A3R5 TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3MR 
       36.95        11.87        42.08        59.57        46.98       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A6EA 
       45.30       145.12        26.89       125.79       137.92        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
       77.56        76.57       144.89        20.38        40.60        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       10.49        43.36        29.29        33.73        14.70         4.96 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29N 
      151.27        78.97        13.97        63.78        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       56.42        61.28        25.87        46.82       115.96        86.14 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
      107.38        75.48        42.77        94.82        21.67        19.76 
TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
       47.28       204.66        96.23       216.66       167.90        43.23 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
      162.48       124.31       122.73        64.04        28.77        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19C 
      127.20        36.95        34.32        51.35         9.17        48.89 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A44A 
       13.02        26.37        49.48        43.82        33.21       174.21 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZR 
       20.91        27.72       357.37        23.93       101.26        11.41 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A3OT 
       49.48        27.02        77.82        80.68        55.59         9.90 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-QB-A6FS 
       15.78        10.13         7.23 

$`USH2A WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       68.15       168.26       340.14        15.45        16.57        16.67 
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-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-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
      115.53       168.00        86.76       113.52        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.48        66.08       130.72        58.06       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       60.23        24.53         9.34        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
       56.35        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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 
       15.39        22.29         9.90        22.95        36.03       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
       33.93       225.96        13.87        10.36        20.35        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 
        7.04        36.46        29.82        27.22         8.65        26.89 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G 
      133.81        91.56        13.55        63.35        85.08        72.07 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       64.64        66.74        14.47       369.93       195.02        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       59.64        39.29        59.28        67.43       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       48.72        54.74        79.66       102.12        13.91        81.21 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       44.88       129.27        28.83        61.51       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
      103.20        16.96       180.39        47.54       248.65        71.21 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       53.26        54.51        41.59       138.81       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19       201.80       134.33       152.81        35.44        13.94 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       77.75        98.40        12.59       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
      131.51        61.05        44.09       162.08        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18       105.07        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-ER-A42L 
       41.56       247.04        93.01        46.98        12.95       149.03 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       92.98        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-A1ZG 
       28.08         7.79        48.85        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.75        47.38        74.73       133.55       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       26.56        27.09        66.67        28.73       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO 
       26.73        54.41        17.46        13.51        19.30        19.43 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         0.20         0.33         0.69 

  USH2A MUTATED USH2A WILD-TYPE 
            2.6             0.2 
  USH2A MUTATED USH2A WILD-TYPE 
         357.37          369.93 
  USH2A MUTATED USH2A WILD-TYPE 
          46.98           56.35 
[1] "2.6 - 357.4 (47.0)" "0.2 - 369.9 (56.4)"
[1] "hr=" "1.2"
D43V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  USH2A MUTATED          4       2       4        3        7       11         2
  USH2A WILD-TYPE        6       4      21        7       18        7         8
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  USH2A MUTATED           4         2        15          3         10
  USH2A WILD-TYPE        10         8        21         11         16
                 vv
clus              STAGE IIIC STAGE IV
  USH2A MUTATED           15        4
  USH2A WILD-TYPE         28       12
D43V4, multiclass
            clus
vv           USH2A MUTATED USH2A WILD-TYPE
  I/II NOS               4               6
  STAGE 0                2               4
  STAGE I                4              21
  STAGE IA               3               7
  STAGE IB               7              18
  STAGE II              11               7
  STAGE IIA              2               8
  STAGE IIB              4              10
  STAGE IIC              2               8
  STAGE III             15              21
  STAGE IIIA             3              11
  STAGE IIIB            10              16
  STAGE IIIC            15              28
  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    37 43 39 36
D43V5, multiclass
       clus
vv      USH2A MUTATED USH2A WILD-TYPE
  T0+T1            16              37
  T2               19              43
  T3               21              39
  T4               19              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USH2A MUTATED    42  18  14  10
  USH2A WILD-TYPE 101  35  20  25
D43V6, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  N0            42             101
  N1            18              35
  N2            14              20
  N3            10              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"
D43V7, binary
                 cls
clus                0   1
  USH2A MUTATED    83   4
  USH2A WILD-TYPE 173  13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     83    4
  USH2A WILD-TYPE  173   13
   clus
vv  USH2A MUTATED USH2A WILD-TYPE
  0            83             173
  1             4              13
[1] 2 2
[1] FALSE
D43V8, binary
                 cls
clus               0  1
  USH2A MUTATED   31 22
  USH2A WILD-TYPE 76 51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     31   22
  USH2A WILD-TYPE   76   51
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             31              76
  YES            22              51
[1] 2 2
[1] FALSE
D43V9, binary
                 cls
clus                0   1
  USH2A MUTATED    17  74
  USH2A WILD-TYPE  20 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     17   74
  USH2A WILD-TYPE   20  179
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             17              20
  YES            74             179
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, binary
                 cls
clus                0   1
  USH2A MUTATED    29  62
  USH2A WILD-TYPE  80 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     29   62
  USH2A WILD-TYPE   80  119
        clus
vv       USH2A MUTATED USH2A WILD-TYPE
  FEMALE            29              80
  MALE              62             119
[1] 2 2
[1] FALSE
D43V12, binary
                 cls
clus                0   1
  USH2A MUTATED    80  11
  USH2A WILD-TYPE 174  24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     80   11
  USH2A WILD-TYPE  174   24
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             80             174
  YES            11              24
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USH2A MUTATED       0                         0    91
  USH2A WILD-TYPE     5                         1   193
D43V13, multiclass
                           clus
vv                          USH2A MUTATED USH2A WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                91             193
[1] 3 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
  USH2A MUTATED     1  90
  USH2A WILD-TYPE   2 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED      1   90
  USH2A WILD-TYPE    2  193
                        clus
vv                       USH2A MUTATED USH2A WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            90             193
[1] 2 2
[1] FALSE

Clustering(44) Variable = XIRP2 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  XIRP2 MUTATED   32 30
  XIRP2 WILD-TYPE 65 73
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             62             138 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             30              73 
$`XIRP2 MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       31.96       166.75       269.03        52.90       134.40        27.35 
TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1QB TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3C6 
       19.04        36.85        62.60        36.30        66.08        58.06 
TCGA-D3-A3MR TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A3Z1 
       90.21        62.70        11.34        42.05        45.70        15.02 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A3F8 
       69.21        76.34       138.67       110.53        64.83        42.64 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29D 
       52.41        13.15        20.38         0.00        75.55        12.99 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GN 
        0.26        47.41        47.74        27.16        30.02        93.63 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MS 
        0.20        81.99        23.77       209.79        94.19       143.93 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-ER-A195 
       23.51        64.04        54.51       111.85       168.85        34.45 
TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A42L TCGA-FS-A1Z3 
       11.47       120.76        22.36        28.67        74.47         8.35 
TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
      130.95         3.06        18.51        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-GN-A268 
       11.54        42.48 

$`XIRP2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       62.07        38.76        33.24         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        76.41        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58        64.83        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1I1 TCGA-DA-A1I2 
       31.76       177.86        22.29        22.85        68.68       150.61 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH 
       60.10        58.85        30.44       225.11         3.91        16.41 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       18.21        24.89        26.24        79.20        75.22        76.14 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       44.28        61.12       346.49       185.19       115.43        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       18.35         0.76        71.31       103.13        15.25         5.75 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
       53.26       124.31       122.73         4.41         6.28        67.89 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       45.90         3.35        19.86       135.98        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        39.81       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.51        49.71        47.18       146.63        73.05 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        4.70        16.87        10.19       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       32.05         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       78.61       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       66.67       173.19        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
       53.29       117.93        96.92        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
            0.0             0.2 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         269.03          346.49 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         47.575          47.050 
[1] "0.0 - 269.0 (47.6)" "0.2 - 346.5 (47.0)"
[1] "hr=" "1.1"
D44V2, survival
                 sevent
clus2               0   1
  XIRP2 MUTATED    45  50
  XIRP2 WILD-TYPE  79 110
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             95             189 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             50             110 
$`XIRP2 MUTATED`
TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       94.98       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 TCGA-D3-A1QB TCGA-D3-A2JD 
       27.35        31.40        50.76        36.95        95.74        11.87 
TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MV 
       42.08        66.08        58.06        46.98       103.59        45.30 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       63.81        26.89       125.79       135.75       137.92        18.18 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV 
       54.67         3.65        15.39         9.90        77.56        76.57 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A3F8 
      144.89        20.38        35.93       135.02        65.92        43.36 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29D 
       58.92        29.82        33.73        14.70       151.27        13.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       63.78        64.64        56.84        56.42        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GN 
       25.87        46.82        59.64        67.43        48.72       102.12 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
       42.77        44.88        94.82        21.67        61.51        47.28 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE 
      268.73       103.20       162.48        71.21        64.04        54.51 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19D 
       41.59       127.20        36.95       201.80        35.44        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH 
       13.02        26.37       162.08        43.82        48.99        41.56 
TCGA-ER-A42L TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZK TCGA-FS-A1ZQ 
      149.03        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        34.03        54.41        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       55.59        13.51        15.78        10.13        62.79 

$`XIRP2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       62.07        46.32        13.87        68.25        54.02        68.15 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        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-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3CB 
       12.10       171.58        66.48        59.57       130.72       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       86.93        60.23        24.53         9.34        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GR 
       55.73        56.35       145.12        32.94        22.62       178.32 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG 
      125.19       151.53         7.10        22.29        25.18        22.95 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       36.03       222.51       176.55        88.87        53.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        33.93        10.49       225.96        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       20.35        29.29         7.04        36.46        27.22         8.65 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       133.81        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
       85.08        78.97        72.07        18.61        66.74       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      195.02        17.92       115.96        39.29        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24       107.38        54.74        79.66        75.48 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       13.91        81.21       129.27        28.83        19.76       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       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       47.54       248.65        43.23        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       28.77        13.81       138.81       172.18        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       53.19        51.35       134.33       152.81        13.94         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       77.75        98.40        48.89       302.07       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        44.09        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
      148.18       105.07        23.34        20.15        28.83       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        33.21        12.95        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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.79       357.37        53.52        46.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38       101.26        74.73        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
       26.56        49.48        27.09        66.67       174.84        26.73 
TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       17.46        19.30         9.90        19.43         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      117.93        96.92        64.44        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.35        10.42        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
            2.6             0.2 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         340.14          369.93 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
          50.76           54.02 
[1] "2.6 - 340.1 (50.8)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.1"
D44V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  XIRP2 MUTATED          3       1       7        5        9       10         6
  XIRP2 WILD-TYPE        7       5      18        5       16        8         4
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  XIRP2 MUTATED           6         2        11          2          8
  XIRP2 WILD-TYPE         8         8        25         12         18
                 vv
clus              STAGE IIIC STAGE IV
  XIRP2 MUTATED           15        5
  XIRP2 WILD-TYPE         28       11
D44V4, multiclass
            clus
vv           XIRP2 MUTATED XIRP2 WILD-TYPE
  I/II NOS               3               7
  STAGE 0                1               5
  STAGE I                7              18
  STAGE IA               5               5
  STAGE IB               9              16
  STAGE II              10               8
  STAGE IIA              6               4
  STAGE IIB              6               8
  STAGE IIC              2               8
  STAGE III             11              25
  STAGE IIIA             2              12
  STAGE IIIB             8              18
  STAGE IIIC            15              28
  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 22 25 18
  XIRP2 WILD-TYPE    36 40 35 37
D44V5, multiclass
       clus
vv      XIRP2 MUTATED XIRP2 WILD-TYPE
  T0+T1            17              36
  T2               22              40
  T3               25              35
  T4               18              37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  XIRP2 MUTATED   54 18 12  8
  XIRP2 WILD-TYPE 89 35 22 27
D44V6, multiclass
    clus
vv   XIRP2 MUTATED XIRP2 WILD-TYPE
  N0            54              89
  N1            18              35
  N2            12              22
  N3             8              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"
D44V7, binary
                 cls
clus                0   1
  XIRP2 MUTATED    90   5
  XIRP2 WILD-TYPE 166  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     90    5
  XIRP2 WILD-TYPE  166   12
   clus
vv  XIRP2 MUTATED XIRP2 WILD-TYPE
  0            90             166
  1             5              12
[1] 2 2
[1] FALSE
D44V8, binary
                 cls
clus               0  1
  XIRP2 MUTATED   41 25
  XIRP2 WILD-TYPE 66 48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     41   25
  XIRP2 WILD-TYPE   66   48
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO             41              66
  YES            25              48
[1] 2 2
[1] FALSE
D44V9, binary
                 cls
clus                0   1
  XIRP2 MUTATED    10  88
  XIRP2 WILD-TYPE  27 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     10   88
  XIRP2 WILD-TYPE   27  165
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO             10              27
  YES            88             165
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, binary
                 cls
clus                0   1
  XIRP2 MUTATED    39  59
  XIRP2 WILD-TYPE  70 122
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     39   59
  XIRP2 WILD-TYPE   70  122
        clus
vv       XIRP2 MUTATED XIRP2 WILD-TYPE
  FEMALE            39              70
  MALE              59             122
[1] 2 2
[1] FALSE
D44V12, binary
                 cls
clus                0   1
  XIRP2 MUTATED    86  12
  XIRP2 WILD-TYPE 168  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     86   12
  XIRP2 WILD-TYPE  168   23
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO             86             168
  YES            12              23
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XIRP2 MUTATED       0                         0    98
  XIRP2 WILD-TYPE     5                         1   186
D44V13, multiclass
                           clus
vv                          XIRP2 MUTATED XIRP2 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                98             186
[1] 3 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
  XIRP2 MUTATED     1  96
  XIRP2 WILD-TYPE   2 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      1   96
  XIRP2 WILD-TYPE    2  187
                        clus
vv                       XIRP2 MUTATED XIRP2 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            96             187
[1] 2 2
[1] FALSE

Clustering(45) Variable = THSD7B MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2               0  1
  THSD7B MUTATED   38 24
  THSD7B WILD-TYPE 59 79
  THSD7B MUTATED THSD7B WILD-TYPE 
              62              138 
  THSD7B MUTATED THSD7B WILD-TYPE 
              24               79 
$`THSD7B MUTATED`
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       62.07       166.75       269.03       134.40        27.35        19.04 
TCGA-FW-A3R5 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2JO TCGA-D3-A3CB 
       36.85        31.89        49.35        62.86        66.08       140.98 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I5 
       90.21        23.67       173.85        69.21        76.34       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C 
       60.10        64.83        42.64        20.38         0.00        75.55 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
       12.99         0.26        44.28        47.41        47.74       346.49 
TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MC 
      115.43        26.14        18.35         0.76         0.20        23.77 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
      171.85        63.25       104.78       227.01       143.93        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19A 
      124.31        64.04        67.89       168.85       135.98         4.54 
TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1ZT 
       59.84        22.36        74.47       174.21       195.98        35.28 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FW-A3TV TCGA-GN-A268 TCGA-GN-A4U4 TCGA-GN-A4U8 
       23.21        18.51        11.54        42.48        34.49        46.92 
TCGA-QB-A6FS TCGA-RP-A693 
        7.23         0.33 

$`THSD7B WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       38.76        33.24        31.96        52.90         8.42        15.72 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
      171.58        64.83        43.53        58.06        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       24.53         9.34        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       138.67        68.68       150.61        58.85        30.44 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
      225.11         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29P 
       24.89        26.24        79.20        75.22        76.14        27.16 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH 
       61.12       185.19        30.02        77.98        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU 
       68.65        10.62        32.48        93.63        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK 
      103.13        15.25         5.75       209.79        94.19        89.26 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      145.45        23.51       122.73         4.41        54.51         6.28 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
      111.85        45.90         3.35        19.86        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       99.06        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       73.05         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1YY 
       68.52        15.48        32.05         4.50       171.78        49.74 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       36.33        78.61       130.95       136.27         4.47         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-OD-A75X TCGA-RP-A690 
       96.92        17.06         7.59       120.53       297.01         0.20 

  THSD7B MUTATED THSD7B WILD-TYPE 
             0.0              0.2 
  THSD7B MUTATED THSD7B WILD-TYPE 
          346.49           312.07 
  THSD7B MUTATED THSD7B WILD-TYPE 
           56.55            44.81 
[1] "0.0 - 346.5 (56.5)" "0.2 - 312.1 (44.8)"
[1] "hr=" "1.7"
D45V2, survival
                  sevent
clus2                0   1
  THSD7B MUTATED    47  43
  THSD7B WILD-TYPE  77 117
  THSD7B MUTATED THSD7B WILD-TYPE 
              90              194 
  THSD7B MUTATED THSD7B WILD-TYPE 
              43              117 
$`THSD7B MUTATED`
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       62.07       168.26         2.60       340.14       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A2J8 
       31.40        50.76        36.95       112.04        71.80        65.49 
TCGA-D3-A2JO TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       66.08        46.98       166.52       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I5 
      174.84       125.19         3.65        77.56        76.57       135.02 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A182 
       88.87        65.92        43.36        29.29        33.73        14.70 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        4.96       151.27        63.35        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       64.64        56.84        18.61        61.28       369.93        25.87 
TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GP 
      115.96        59.28        67.43        48.72        75.48        13.91 
TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MJ 
       42.77        21.67        61.51        47.28       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      216.66        47.54       248.65       162.48        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JB 
       64.04        41.59       172.18        36.95        53.19       201.80 
TCGA-EE-A3JI TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A42L TCGA-FR-A44A 
      152.81        77.75        61.05        43.82       149.03       174.21 
TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 
      202.65         7.79        74.73        53.16        49.48        77.82 
TCGA-FS-A4F5 TCGA-FS-A4FC TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       28.73        54.41        13.51        15.78        10.13        62.79 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       39.35        10.42        48.89         7.23         0.33         0.69 

$`THSD7B WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A2GO TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
      126.81        15.45        16.57        16.67       112.57       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        66.48        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51F 
       58.06        86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 
      125.79       135.75       137.92       178.32        18.18       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       35.93        53.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
      225.96        13.87        10.36        20.35        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A20B 
       36.46        29.82        27.22         8.65        26.89       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29P TCGA-EE-A29Q 
       91.56        13.55        85.08        78.97        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
       14.47       195.02        17.92        46.82        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       86.14       173.79       220.24       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
      102.12        81.21        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-A2MK 
       19.76       103.27       268.73       103.20        16.96       180.39 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
      167.90        43.23        71.21       122.73        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE 
       13.81       138.81       127.20        64.08        34.32        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      134.33        35.44        13.94         9.17        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18       105.07        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       92.98        15.72       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08        27.72        48.85       357.37        53.52        46.45 
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        34.03        26.73        80.68        17.46        55.59 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        19.43         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U9 
       96.92        64.44        32.48        48.00       121.91        22.13 
TCGA-OD-A75X TCGA-RP-A690 
      297.90         0.20 

  THSD7B MUTATED THSD7B WILD-TYPE 
            0.33             0.20 
  THSD7B MUTATED THSD7B WILD-TYPE 
          369.93           357.37 
  THSD7B MUTATED THSD7B WILD-TYPE 
          61.165           50.185 
[1] "0.3 - 369.9 (61.2)" "0.2 - 357.4 (50.2)"
[1] "hr=" "1.4"
D45V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  THSD7B MUTATED          4       1       7        5        9        8
  THSD7B WILD-TYPE        6       5      18        5       16       10
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  THSD7B MUTATED           3         6         1        13          4
  THSD7B WILD-TYPE         7         8         9        23         10
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  THSD7B MUTATED           11         10        5
  THSD7B WILD-TYPE         15         33       11
D45V4, multiclass
            clus
vv           THSD7B MUTATED THSD7B WILD-TYPE
  I/II NOS                4                6
  STAGE 0                 1                5
  STAGE I                 7               18
  STAGE IA                5                5
  STAGE IB                9               16
  STAGE II                8               10
  STAGE IIA               3                7
  STAGE IIB               6                8
  STAGE IIC               1                9
  STAGE III              13               23
  STAGE IIIA              4               10
  STAGE IIIB             11               15
  STAGE IIIC             10               33
  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      17 27 18 15
  THSD7B WILD-TYPE    36 35 42 40
D45V5, multiclass
       clus
vv      THSD7B MUTATED THSD7B WILD-TYPE
  T0+T1             17               36
  T2                27               35
  T3                18               42
  T4                15               40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  THSD7B MUTATED   46 19 13  5
  THSD7B WILD-TYPE 97 34 21 30
D45V6, multiclass
    clus
vv   THSD7B MUTATED THSD7B WILD-TYPE
  N0             46               97
  N1             19               34
  N2             13               21
  N3              5               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"
D45V7, binary
                  cls
clus                 0   1
  THSD7B MUTATED    84   5
  THSD7B WILD-TYPE 172  12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     84    5
  THSD7B WILD-TYPE  172   12
   clus
vv  THSD7B MUTATED THSD7B WILD-TYPE
  0             84              172
  1              5               12
[1] 2 2
[1] FALSE
D45V8, binary
                  cls
clus                0  1
  THSD7B MUTATED   39 18
  THSD7B WILD-TYPE 68 55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     39   18
  THSD7B WILD-TYPE   68   55
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  NO              39               68
  YES             18               55
[1] 2 2
[1] FALSE
D45V9, binary
                  cls
clus                 0   1
  THSD7B MUTATED    14  78
  THSD7B WILD-TYPE  23 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     14   78
  THSD7B WILD-TYPE   23  175
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  NO              14               23
  YES             78              175
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, binary
                  cls
clus                 0   1
  THSD7B MUTATED    27  65
  THSD7B WILD-TYPE  82 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     27   65
  THSD7B WILD-TYPE   82  116
        clus
vv       THSD7B MUTATED THSD7B WILD-TYPE
  FEMALE             27               82
  MALE               65              116
[1] 2 2
[1] FALSE
D45V12, binary
                  cls
clus                 0   1
  THSD7B MUTATED    84   8
  THSD7B WILD-TYPE 170  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED     84    8
  THSD7B WILD-TYPE  170   27
     clus
vv    THSD7B MUTATED THSD7B WILD-TYPE
  NO              84              170
  YES              8               27
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THSD7B MUTATED       0                         0    92
  THSD7B WILD-TYPE     5                         1   192
D45V13, multiclass
                           clus
vv                          THSD7B MUTATED THSD7B WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 92              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"
D45V14, binary
                  cls
clus                 0   1
  THSD7B MUTATED     0  91
  THSD7B WILD-TYPE   3 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THSD7B MUTATED      0   91
  THSD7B WILD-TYPE    3  192
                        clus
vv                       THSD7B MUTATED THSD7B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             91              192
[1] 2 2
[1] FALSE

Clustering(46) Variable = USP17L2 MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  USP17L2 MUTATED    8  7
  USP17L2 WILD-TYPE 89 96
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               15               185 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
                7                96 
$`USP17L2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A3CB 
       62.07       134.40        19.04        36.85        49.35       140.98 
TCGA-D9-A6EC TCGA-EB-A5KH TCGA-EE-A181 TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2MJ 
       69.21        16.41        20.38        47.74        30.02        63.25 
TCGA-ER-A199 TCGA-FS-A1ZD TCGA-FS-A4F9 
        7.82        32.78        13.28 

$`USP17L2 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       27.35         8.42        15.72        31.89       110.93       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       19.04        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        66.08        43.53        58.06        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        15.02        22.29        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 
       30.44       225.11        42.64         3.91        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        24.89         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       27.16        61.12       346.49       185.19       115.43        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
      171.85        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
      168.85        19.86       135.98        34.45        10.49         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      312.07        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       18.51        66.67       173.19        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  USP17L2 MUTATED USP17L2 WILD-TYPE 
             7.82              0.00 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
           140.98            346.49 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
            36.85             47.41 
[1] "7.8 - 141.0 (36.9)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.3"
D46V2, survival
                   sevent
clus2                 0   1
  USP17L2 MUTATED     9  12
  USP17L2 WILD-TYPE 115 148
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               21               263 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
               12               148 
$`USP17L2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A3CB 
       62.07       134.40        31.40        36.95        71.80       166.52 
TCGA-D9-A6EC TCGA-DA-A1I4 TCGA-EB-A5KH TCGA-EE-A181 TCGA-EE-A29M TCGA-EE-A2A2 
       77.56        35.93        20.35        33.73        56.84        59.64 
TCGA-EE-A2GI TCGA-EE-A2MJ TCGA-EE-A3AH TCGA-ER-A199 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       48.72        96.23       138.81         9.17        48.85        53.52 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-GN-A266 
       28.73        34.03        10.13 

$`USP17L2 WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A198 
      168.26         2.60       340.14       126.81        27.35        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       15.45        16.57        16.67       112.04       112.57       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        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE 
       59.57       130.72        58.06        46.98        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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29         9.90        25.18        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       222.51       176.55       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN 
      225.96        43.36        13.87        10.36        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
        7.04        36.46        29.82        27.22         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
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       173.79       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       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-A195 
       53.19       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       13.94        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       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        46.45         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-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
      174.84        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        96.92        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  USP17L2 MUTATED USP17L2 WILD-TYPE 
             9.17              0.20 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
           166.52            369.93 
  USP17L2 MUTATED USP17L2 WILD-TYPE 
            48.85             54.41 
[1] "9.2 - 166.5 (48.9)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.3"
D46V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  USP17L2 MUTATED          1       0       1        2        2        3
  USP17L2 WILD-TYPE        9       6      24        8       23       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  USP17L2 MUTATED           1         1         0         4          1
  USP17L2 WILD-TYPE         9        13        10        32         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  USP17L2 MUTATED            0          4        1
  USP17L2 WILD-TYPE         26         39       15
D46V4, multiclass
            clus
vv           USP17L2 MUTATED USP17L2 WILD-TYPE
  I/II NOS                 1                 9
  STAGE 0                  0                 6
  STAGE I                  1                24
  STAGE IA                 2                 8
  STAGE IB                 2                23
  STAGE II                 3                15
  STAGE IIA                1                 9
  STAGE IIB                1                13
  STAGE IIC                0                10
  STAGE III                4                32
  STAGE IIIA               1                13
  STAGE IIIB               0                26
  STAGE IIIC               4                39
  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    50 57 54 50
D46V5, multiclass
       clus
vv      USP17L2 MUTATED USP17L2 WILD-TYPE
  T0+T1               3                50
  T2                  5                57
  T3                  6                54
  T4                  5                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  USP17L2 MUTATED    12   4   2   2
  USP17L2 WILD-TYPE 131  49  32  33
D46V6, multiclass
    clus
vv   USP17L2 MUTATED USP17L2 WILD-TYPE
  N0              12               131
  N1               4                49
  N2               2                32
  N3               2                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"
D46V7, binary
                   cls
clus                  0   1
  USP17L2 MUTATED    20   1
  USP17L2 WILD-TYPE 236  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED     20    1
  USP17L2 WILD-TYPE  236   16
   clus
vv  USP17L2 MUTATED USP17L2 WILD-TYPE
  0              20               236
  1               1                16
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                 0  1
  USP17L2 MUTATED   10  5
  USP17L2 WILD-TYPE 97 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED     10    5
  USP17L2 WILD-TYPE   97   68
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  NO               10                97
  YES               5                68
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     1  21
  USP17L2 WILD-TYPE  36 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      1   21
  USP17L2 WILD-TYPE   36  232
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  NO                1                36
  YES              21               232
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     4  18
  USP17L2 WILD-TYPE 105 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      4   18
  USP17L2 WILD-TYPE  105  163
        clus
vv       USP17L2 MUTATED USP17L2 WILD-TYPE
  FEMALE               4               105
  MALE                18               163
[1] 2 2
[1] FALSE
D46V12, binary
                   cls
clus                  0   1
  USP17L2 MUTATED    20   2
  USP17L2 WILD-TYPE 234  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED     20    2
  USP17L2 WILD-TYPE  234   33
     clus
vv    USP17L2 MUTATED USP17L2 WILD-TYPE
  NO               20               234
  YES               2                33
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP17L2 MUTATED       1                         0    21
  USP17L2 WILD-TYPE     4                         1   263
D46V13, multiclass
                           clus
vv                          USP17L2 MUTATED USP17L2 WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  21               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"
D46V14, binary
                   cls
clus                  0   1
  USP17L2 MUTATED     0  22
  USP17L2 WILD-TYPE   3 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  USP17L2 MUTATED      0   22
  USP17L2 WILD-TYPE    3  261
                        clus
vv                       USP17L2 MUTATED USP17L2 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              22               261
[1] 2 2
[1] FALSE

Clustering(47) Variable = S100A8 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2                0   1
  S100A8 MUTATED     2   3
  S100A8 WILD-TYPE  95 100
  S100A8 MUTATED S100A8 WILD-TYPE 
               5              195 
  S100A8 MUTATED S100A8 WILD-TYPE 
               3              100 
$`S100A8 MUTATED`
TCGA-EE-A182 TCGA-EE-A3AE TCGA-ER-A19N TCGA-FS-A1ZZ TCGA-QB-A6FS 
        0.00        54.51        42.51         3.06         7.23 

$`S100A8 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
      177.86        15.02        22.29        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 
       52.41        18.21        13.15        24.89        20.38        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        64.04         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       35.28         4.47        23.21         5.29        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
      297.01         0.20         0.33 

  S100A8 MUTATED S100A8 WILD-TYPE 
             0.0              0.2 
  S100A8 MUTATED S100A8 WILD-TYPE 
           54.51           346.49 
  S100A8 MUTATED S100A8 WILD-TYPE 
            7.23            47.74 
[1] "0.0 - 54.5 (7.2)"   "0.2 - 346.5 (47.7)"
[1] "hr=" "3.9"
D47V2, survival
                  sevent
clus2                0   1
  S100A8 MUTATED     2   5
  S100A8 WILD-TYPE 122 155
  S100A8 MUTATED S100A8 WILD-TYPE 
               7              277 
  S100A8 MUTATED S100A8 WILD-TYPE 
               5              155 
$`S100A8 MUTATED`
TCGA-EE-A182 TCGA-EE-A2M5 TCGA-EE-A3AE TCGA-ER-A19N TCGA-FS-A1ZZ TCGA-GN-A266 
       14.70        21.67        54.51        44.09        27.02        10.13 
TCGA-QB-A6FS 
        7.23 

$`S100A8 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        33.73        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        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       180.39       216.66       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-A3AF TCGA-EE-A3AG 
      124.31       122.73        64.04        28.77        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       10.42        48.89        22.13       297.90         0.20         0.33 
TCGA-RP-A694 
        0.69 

  S100A8 MUTATED S100A8 WILD-TYPE 
            7.23             0.20 
  S100A8 MUTATED S100A8 WILD-TYPE 
           54.51           369.93 
  S100A8 MUTATED S100A8 WILD-TYPE 
           21.67            54.67 
[1] "7.2 - 54.5 (21.7)"  "0.2 - 369.9 (54.7)"
[1] "hr=" "3.8"
D47V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  S100A8 MUTATED          1       0       1        1        0        0
  S100A8 WILD-TYPE        9       6      24        9       25       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  S100A8 MUTATED           0         1         0         0          0
  S100A8 WILD-TYPE        10        13        10        36         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  S100A8 MUTATED            0          2        0
  S100A8 WILD-TYPE         26         41       16
D47V4, multiclass
            clus
vv           S100A8 MUTATED S100A8 WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                1                9
  STAGE IB                0               25
  STAGE II                0               18
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               0               36
  STAGE IIIA              0               14
  STAGE IIIB              0               26
  STAGE IIIC              2               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
  S100A8 MUTATED       2  2  1  1
  S100A8 WILD-TYPE    51 60 59 54
D47V5, multiclass
       clus
vv      S100A8 MUTATED S100A8 WILD-TYPE
  T0+T1              2               51
  T2                 2               60
  T3                 1               59
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  S100A8 MUTATED     4   1   0   1
  S100A8 WILD-TYPE 139  52  34  34
D47V6, multiclass
    clus
vv   S100A8 MUTATED S100A8 WILD-TYPE
  N0              4              139
  N1              1               52
  N2              0               34
  N3              1               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"
D47V7, binary
                  cls
clus                 0   1
  S100A8 MUTATED     6   0
  S100A8 WILD-TYPE 250  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A8 MUTATED      6    0
  S100A8 WILD-TYPE  250   17
   clus
vv  S100A8 MUTATED S100A8 WILD-TYPE
  0              6              250
  1              0               17
[1] 2 2
[1] FALSE
D47V8, binary
                  cls
clus                 0   1
  S100A8 MUTATED     2   2
  S100A8 WILD-TYPE 105  71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A8 MUTATED      2    2
  S100A8 WILD-TYPE  105   71
     clus
vv    S100A8 MUTATED S100A8 WILD-TYPE
  NO               2              105
  YES              2               71
[1] 2 2
[1] FALSE
D47V9, binary
                  cls
clus                 0   1
  S100A8 MUTATED     3   5
  S100A8 WILD-TYPE  34 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A8 MUTATED      3    5
  S100A8 WILD-TYPE   34  248
     clus
vv    S100A8 MUTATED S100A8 WILD-TYPE
  NO               3               34
  YES              5              248
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, binary
                  cls
clus                 0   1
  S100A8 MUTATED     4   4
  S100A8 WILD-TYPE 105 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A8 MUTATED      4    4
  S100A8 WILD-TYPE  105  177
        clus
vv       S100A8 MUTATED S100A8 WILD-TYPE
  FEMALE              4              105
  MALE                4              177
[1] 2 2
[1] FALSE
D47V12, binary
                  cls
clus                 0   1
  S100A8 MUTATED     5   3
  S100A8 WILD-TYPE 249  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A8 MUTATED      5    3
  S100A8 WILD-TYPE  249   32
     clus
vv    S100A8 MUTATED S100A8 WILD-TYPE
  NO               5              249
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  S100A8 MUTATED       0                         0     8
  S100A8 WILD-TYPE     5                         1   276
D47V13, multiclass
                           clus
vv                          S100A8 MUTATED S100A8 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                  cls
clus                 0   1
  S100A8 MUTATED     1   7
  S100A8 WILD-TYPE   2 276
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A8 MUTATED      1    7
  S100A8 WILD-TYPE    2  276
                        clus
vv                       S100A8 MUTATED S100A8 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO              7              276
[1] 2 2
[1] FALSE

Clustering(48) Variable = CTNNB1 MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED    4  7
  CTNNB1 WILD-TYPE 93 96
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              11              189 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               7               96 
$`CTNNB1 MUTATED`
TCGA-EE-A180 TCGA-D3-A1Q5 TCGA-D3-A2JN TCGA-D9-A6EC TCGA-D9-A6EG TCGA-EE-A181 
       31.96       110.93        64.83        69.21        22.85        20.38 
TCGA-EE-A182 TCGA-EE-A2M6 TCGA-EE-A3AC TCGA-FS-A1YY TCGA-FS-A4F9 
        0.00       103.13        64.04        49.74        13.28 

$`CTNNB1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      134.40        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
      107.61        36.30       171.58        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A183 
       16.41        52.41        18.21        13.15        24.89        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76         0.20        71.31        81.99        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
             0.0              0.2 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          110.93           346.49 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           49.74            47.18 
[1] "0.0 - 110.9 (49.7)" "0.2 - 346.5 (47.2)"
[1] "hr=" "1.7"
D48V2, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED     7   8
  CTNNB1 WILD-TYPE 117 152
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              15              269 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8              152 
$`CTNNB1 MUTATED`
TCGA-EB-A5SH TCGA-EE-A180 TCGA-D3-A1Q5 TCGA-D3-A2JN TCGA-D9-A149 TCGA-D9-A6E9 
       54.02        94.98       112.57        66.48        54.67         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29A TCGA-EE-A2M6 
       77.56        22.95        33.73        14.70        63.35       129.27 
TCGA-EE-A3AC TCGA-FS-A1YY TCGA-FS-A4F9 
       64.04       228.59        34.03 

$`CTNNB1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A184 TCGA-EE-A20H 
       62.07        46.32        13.87        68.25        68.15       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
        2.60       340.14       126.81       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       113.52        42.08        12.10       171.58 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       15.39        22.29        25.18        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      216.66       167.90        47.54       248.65        43.23       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        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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        46.45 
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        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
             9.9              0.2 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          228.59           369.93 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           63.35            53.26 
[1] "9.9 - 228.6 (63.4)" "0.2 - 369.9 (53.3)"
[1] "hr=" "1"  
D48V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  CTNNB1 MUTATED          1       0       1        0        0        1
  CTNNB1 WILD-TYPE        9       6      24       10       25       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CTNNB1 MUTATED           1         0         0         4          4
  CTNNB1 WILD-TYPE         9        14        10        32         10
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CTNNB1 MUTATED            1          2        0
  CTNNB1 WILD-TYPE         25         41       16
D48V4, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                0               10
  STAGE IB                0               25
  STAGE II                1               17
  STAGE IIA               1                9
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               4               32
  STAGE IIIA              4               10
  STAGE IIIB              1               25
  STAGE IIIC              2               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
  CTNNB1 MUTATED       3  0  6  5
  CTNNB1 WILD-TYPE    50 62 54 50
D48V5, multiclass
       clus
vv      CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T0+T1              3               50
  T2                 0               62
  T3                 6               54
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CTNNB1 MUTATED     6   8   1   1
  CTNNB1 WILD-TYPE 137  45  33  34
D48V6, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0              6              137
  N1              8               45
  N2              1               33
  N3              1               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"
D48V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    16   0
  CTNNB1 WILD-TYPE 240  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     16    0
  CTNNB1 WILD-TYPE  240   17
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             16              240
  1              0               17
[1] 2 2
[1] FALSE
D48V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     7   4
  CTNNB1 WILD-TYPE 100  69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      7    4
  CTNNB1 WILD-TYPE  100   69
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               7              100
  YES              4               69
[1] 2 2
[1] FALSE
D48V9, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     2  14
  CTNNB1 WILD-TYPE  35 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      2   14
  CTNNB1 WILD-TYPE   35  239
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               2               35
  YES             14              239
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     7   9
  CTNNB1 WILD-TYPE 102 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      7    9
  CTNNB1 WILD-TYPE  102  172
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              7              102
  MALE                9              172
[1] 2 2
[1] FALSE
D48V12, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    16   0
  CTNNB1 WILD-TYPE 238  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     16    0
  CTNNB1 WILD-TYPE  238   35
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              16              238
  YES              0               35
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED       0                         0    16
  CTNNB1 WILD-TYPE     5                         1   268
D48V13, multiclass
                           clus
vv                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 16              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"
D48V14, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0  15
  CTNNB1 WILD-TYPE   3 268
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0   15
  CTNNB1 WILD-TYPE    3  268
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             15              268
[1] 2 2
[1] FALSE

Clustering(49) Variable = USP9X MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2              0  1
  USP9X MUTATED    6  4
  USP9X WILD-TYPE 91 99
  USP9X MUTATED USP9X WILD-TYPE 
             10             190 
  USP9X MUTATED USP9X WILD-TYPE 
              4              99 
$`USP9X MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-EE-A2MF TCGA-EE-A3AF 
      134.40        36.85        69.21        76.34       209.79         6.28 
TCGA-EE-A3J7 TCGA-ER-A19P TCGA-ER-A42L TCGA-FS-A1Z0 
       45.90       120.76        74.47       195.98 

$`USP9X WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.29        22.85       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG 
       81.99       103.13        15.25         5.75        23.77        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB 
        4.41        54.51        67.89       111.85         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84        42.51        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       68.52        15.48        32.05         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  USP9X MUTATED USP9X WILD-TYPE 
           6.28            0.00 
  USP9X MUTATED USP9X WILD-TYPE 
         209.79          346.49 
  USP9X MUTATED USP9X WILD-TYPE 
         75.405          46.455 
[1] "6.3 - 209.8 (75.4)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.9"
D49V2, survival
                 sevent
clus2               0   1
  USP9X MUTATED     9   7
  USP9X WILD-TYPE 115 153
  USP9X MUTATED USP9X WILD-TYPE 
             16             268 
  USP9X MUTATED USP9X WILD-TYPE 
              7             153 
$`USP9X MUTATED`
TCGA-EE-A2MR TCGA-ER-A198 TCGA-FW-A3R5 TCGA-D3-A3C7 TCGA-D9-A148 TCGA-D9-A6EC 
      134.40        50.76        36.95        46.98       151.53        77.56 
TCGA-DA-A1HV TCGA-EE-A2MF TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A19P TCGA-ER-A2NH 
       76.57       268.73        13.81        64.08       162.08        41.56 
TCGA-ER-A42L TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F5 
      149.03       202.65        23.93        28.73 

$`USP9X WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       126.81        27.35 
TCGA-ER-A193 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       31.40        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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-A3CB 
       66.48        66.08        59.57       130.72        58.06       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW 
       15.39        22.29         9.90        25.18        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       180.39       216.66       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-A3AG 
      124.31       122.73        64.04        28.77        54.51        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       172.18       127.20        36.95        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       43.82        23.34        20.15        28.83        48.99       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       93.01        46.98        33.21        12.95        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        46.45 
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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  USP9X MUTATED USP9X WILD-TYPE 
          13.81            0.20 
  USP9X MUTATED USP9X WILD-TYPE 
         268.73          369.93 
  USP9X MUTATED USP9X WILD-TYPE 
         70.325          53.720 
[1] "13.8 - 268.7 (70.3)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1.7"
D49V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  USP9X MUTATED          0       1       3        1        1        2         0
  USP9X WILD-TYPE       10       5      22        9       24       16        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  USP9X MUTATED           0         0         2          1          1
  USP9X WILD-TYPE        14        10        34         13         25
                 vv
clus              STAGE IIIC STAGE IV
  USP9X MUTATED            2        0
  USP9X WILD-TYPE         41       16
D49V4, multiclass
            clus
vv           USP9X MUTATED USP9X WILD-TYPE
  I/II NOS               0              10
  STAGE 0                1               5
  STAGE I                3              22
  STAGE IA               1               9
  STAGE IB               1              24
  STAGE II               2              16
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              2              34
  STAGE IIIA             1              13
  STAGE IIIB             1              25
  STAGE IIIC             2              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
  USP9X MUTATED       4  4  3  1
  USP9X WILD-TYPE    49 58 57 54
D49V5, multiclass
       clus
vv      USP9X MUTATED USP9X WILD-TYPE
  T0+T1             4              49
  T2                4              58
  T3                3              57
  T4                1              54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP9X MUTATED     9   2   2   3
  USP9X WILD-TYPE 134  51  32  32
D49V6, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  N0             9             134
  N1             2              51
  N2             2              32
  N3             3              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"
D49V7, binary
                 cls
clus                0   1
  USP9X MUTATED    16   1
  USP9X WILD-TYPE 240  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     16    1
  USP9X WILD-TYPE  240   16
   clus
vv  USP9X MUTATED USP9X WILD-TYPE
  0            16             240
  1             1              16
[1] 2 2
[1] FALSE
D49V8, binary
                 cls
clus                0   1
  USP9X MUTATED     7   2
  USP9X WILD-TYPE 100  71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      7    2
  USP9X WILD-TYPE  100   71
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO              7             100
  YES             2              71
[1] 2 2
[1] FALSE
D49V9, binary
                 cls
clus                0   1
  USP9X MUTATED     3  14
  USP9X WILD-TYPE  34 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      3   14
  USP9X WILD-TYPE   34  239
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO              3              34
  YES            14             239
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, binary
                 cls
clus                0   1
  USP9X MUTATED     7  10
  USP9X WILD-TYPE 102 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      7   10
  USP9X WILD-TYPE  102  171
        clus
vv       USP9X MUTATED USP9X WILD-TYPE
  FEMALE             7             102
  MALE              10             171
[1] 2 2
[1] FALSE
D49V12, binary
                 cls
clus                0   1
  USP9X MUTATED    14   3
  USP9X WILD-TYPE 240  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     14    3
  USP9X WILD-TYPE  240   32
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO             14             240
  YES             3              32
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP9X MUTATED       0                         0    17
  USP9X WILD-TYPE     5                         1   267
D49V13, multiclass
                           clus
vv                          USP9X MUTATED USP9X WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                17             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"
D49V14, binary
                 cls
clus                0   1
  USP9X MUTATED     0  17
  USP9X WILD-TYPE   3 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED      0   17
  USP9X WILD-TYPE    3  266
                        clus
vv                       USP9X MUTATED USP9X WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            17             266
[1] 2 2
[1] FALSE

Clustering(50) Variable = C10ORF28 MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                  0   1
  C10ORF28 MUTATED     5   1
  C10ORF28 WILD-TYPE  92 102
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 6                194 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 1                102 
$`C10ORF28 MUTATED`
TCGA-EB-A5SG TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A3AA TCGA-FR-A3YN TCGA-FS-A4FD 
       33.24         0.26        47.74       124.31         4.50        80.68 

$`C10ORF28 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      134.40        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       75.55        79.20        75.22        76.14        12.99        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      145.45       227.01       143.93        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       32.05        74.47       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
              0.26               0.00 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
            124.31             346.49 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
            40.490             47.295 
[1] "0.3 - 124.3 (40.5)" "0.0 - 346.5 (47.3)"
[1] "hr=" "2.2"
D50V2, survival
                    sevent
clus2                  0   1
  C10ORF28 MUTATED     6   1
  C10ORF28 WILD-TYPE 118 159
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 7                277 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 1                159 
$`C10ORF28 MUTATED`
TCGA-EB-A5SG TCGA-D3-A5GO TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A3AA TCGA-FR-A3YN 
       68.25       137.92        63.78        56.84       124.31        92.98 
TCGA-FS-A4FD 
       80.68 

$`C10ORF28 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        13.87        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      125.79       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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        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       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21        53.26       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         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-FW-A3I3 
       28.73       174.84        34.03        26.73        54.41        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
             56.84               0.20 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
            137.92             369.93 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
             80.68              53.19 
[1] "56.8 - 137.9 (80.7)" "0.2 - 369.9 (53.2)" 
[1] "hr=" "4.9"
D50V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C10ORF28 MUTATED          0       0       0        0        2        1
  C10ORF28 WILD-TYPE       10       6      25       10       23       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C10ORF28 MUTATED           0         0         0         1          0
  C10ORF28 WILD-TYPE        10        14        10        35         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C10ORF28 MUTATED            1          1        0
  C10ORF28 WILD-TYPE         25         42       16
D50V4, multiclass
            clus
vv           C10ORF28 MUTATED C10ORF28 WILD-TYPE
  I/II NOS                  0                 10
  STAGE 0                   0                  6
  STAGE I                   0                 25
  STAGE IA                  0                 10
  STAGE IB                  2                 23
  STAGE II                  1                 17
  STAGE IIA                 0                 10
  STAGE IIB                 0                 14
  STAGE IIC                 0                 10
  STAGE III                 1                 35
  STAGE IIIA                0                 14
  STAGE IIIB                1                 25
  STAGE IIIC                1                 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
  C10ORF28 MUTATED       1  3  1  1
  C10ORF28 WILD-TYPE    52 59 59 54
D50V5, multiclass
       clus
vv      C10ORF28 MUTATED C10ORF28 WILD-TYPE
  T0+T1                1                 52
  T2                   3                 59
  T3                   1                 59
  T4                   1                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C10ORF28 MUTATED     3   1   1   1
  C10ORF28 WILD-TYPE 140  52  33  34
D50V6, multiclass
    clus
vv   C10ORF28 MUTATED C10ORF28 WILD-TYPE
  N0                3                140
  N1                1                 52
  N2                1                 33
  N3                1                 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"
D50V7, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     6   0
  C10ORF28 WILD-TYPE 250  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      6    0
  C10ORF28 WILD-TYPE  250   17
   clus
vv  C10ORF28 MUTATED C10ORF28 WILD-TYPE
  0                6                250
  1                0                 17
[1] 2 2
[1] FALSE
D50V8, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     4   0
  C10ORF28 WILD-TYPE 103  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      4    0
  C10ORF28 WILD-TYPE  103   73
     clus
vv    C10ORF28 MUTATED C10ORF28 WILD-TYPE
  NO                 4                103
  YES                0                 73
[1] 2 2
[1] FALSE
D50V9, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     1   6
  C10ORF28 WILD-TYPE  36 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      1    6
  C10ORF28 WILD-TYPE   36  247
     clus
vv    C10ORF28 MUTATED C10ORF28 WILD-TYPE
  NO                 1                 36
  YES                6                247
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     2   5
  C10ORF28 WILD-TYPE 107 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      2    5
  C10ORF28 WILD-TYPE  107  176
        clus
vv       C10ORF28 MUTATED C10ORF28 WILD-TYPE
  FEMALE                2                107
  MALE                  5                176
[1] 2 2
[1] FALSE
D50V12, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     7   0
  C10ORF28 WILD-TYPE 247  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      7    0
  C10ORF28 WILD-TYPE  247   35
     clus
vv    C10ORF28 MUTATED C10ORF28 WILD-TYPE
  NO                 7                247
  YES                0                 35
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C10ORF28 MUTATED       0                         0     7
  C10ORF28 WILD-TYPE     5                         1   277
D50V13, multiclass
                           clus
vv                          C10ORF28 MUTATED C10ORF28 WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     0   7
  C10ORF28 WILD-TYPE   3 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      0    7
  C10ORF28 WILD-TYPE    3  276
                        clus
vv                       C10ORF28 MUTATED C10ORF28 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                7                276
[1] 2 2
[1] FALSE

Clustering(51) Variable = MAN1A1 MUTATION ANALYSIS
D51V1, survival
                  sevent
clus2               0  1
  MAN1A1 MUTATED    4  5
  MAN1A1 WILD-TYPE 93 98
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
               9              191 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
               5               98 
$`MAN1A1 MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-EE-A29E TCGA-EE-A3AC 
      134.40        27.35        36.85        62.86         0.26        64.04 
TCGA-EE-A3J4 TCGA-ER-A199 TCGA-FS-A1ZC 
      111.85         7.82       312.07 

$`MAN1A1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.90        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       45.99        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       42.05        45.70       177.86        15.02        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14        12.99        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      143.93        23.51        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28        67.89        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
       19.86       135.98        34.45        10.49         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD 
      171.78        49.74       195.98         8.35        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
            0.26             0.00 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
          312.07           346.49 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
           62.86            47.18 
[1] "0.3 - 312.1 (62.9)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.3"
D51V2, survival
                  sevent
clus2                0   1
  MAN1A1 MUTATED     7   8
  MAN1A1 WILD-TYPE 117 152
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
              15              269 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
               8              152 
$`MAN1A1 MUTATED`
TCGA-D3-A3ML TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-D3-A3C7 
       13.87       134.40        27.35        36.95        65.49        46.98 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-ER-A199 
       63.78        18.61        64.04       127.20        36.95         9.17 
TCGA-FS-A1ZC TCGA-GF-A6C9 TCGA-RP-A694 
      357.37        15.78         0.69 

$`MAN1A1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 TCGA-ER-A198 
      168.26         2.60       340.14       126.81        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        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        66.48        66.08 
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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       78.97        13.97        72.07        64.64        56.84        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      138.81       172.18        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-A19A 
       51.35       134.33       152.81        35.44        13.94        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       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       22.13       297.90         7.23         0.20         0.33 

  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
            0.69             0.20 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
          357.37           369.93 
  MAN1A1 MUTATED MAN1A1 WILD-TYPE 
           36.95            54.41 
[1] "0.7 - 357.4 (37.0)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1"  
D51V3, continuous
                  vv
clus               I/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      24       10       24       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MAN1A1 MUTATED           0         0         0         5          1
  MAN1A1 WILD-TYPE        10        14        10        31         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAN1A1 MUTATED            2          1        1
  MAN1A1 WILD-TYPE         24         42       15
D51V4, multiclass
            clus
vv           MAN1A1 MUTATED MAN1A1 WILD-TYPE
  I/II NOS                2                8
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                0               10
  STAGE IB                1               24
  STAGE II                1               17
  STAGE IIA               0               10
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               5               31
  STAGE IIIA              1               13
  STAGE IIIB              2               24
  STAGE IIIC              1               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
  MAN1A1 MUTATED       2  2  3  2
  MAN1A1 WILD-TYPE    51 60 57 53
D51V5, multiclass
       clus
vv      MAN1A1 MUTATED MAN1A1 WILD-TYPE
  T0+T1              2               51
  T2                 2               60
  T3                 3               57
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAN1A1 MUTATED     5   3   4   1
  MAN1A1 WILD-TYPE 138  50  30  34
D51V6, multiclass
    clus
vv   MAN1A1 MUTATED MAN1A1 WILD-TYPE
  N0              5              138
  N1              3               50
  N2              4               30
  N3              1               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"
D51V7, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED    13   1
  MAN1A1 WILD-TYPE 243  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED     13    1
  MAN1A1 WILD-TYPE  243   16
   clus
vv  MAN1A1 MUTATED MAN1A1 WILD-TYPE
  0             13              243
  1              1               16
[1] 2 2
[1] FALSE
D51V8, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     5   2
  MAN1A1 WILD-TYPE 102  71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      5    2
  MAN1A1 WILD-TYPE  102   71
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  NO               5              102
  YES              2               71
[1] 2 2
[1] FALSE
D51V9, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     5  10
  MAN1A1 WILD-TYPE  32 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      5   10
  MAN1A1 WILD-TYPE   32  243
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  NO               5               32
  YES             10              243
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED     2  13
  MAN1A1 WILD-TYPE 107 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      2   13
  MAN1A1 WILD-TYPE  107  168
        clus
vv       MAN1A1 MUTATED MAN1A1 WILD-TYPE
  FEMALE              2              107
  MALE               13              168
[1] 2 2
[1] FALSE
D51V12, binary
                  cls
clus                 0   1
  MAN1A1 MUTATED    13   2
  MAN1A1 WILD-TYPE 241  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED     13    2
  MAN1A1 WILD-TYPE  241   33
     clus
vv    MAN1A1 MUTATED MAN1A1 WILD-TYPE
  NO              13              241
  YES              2               33
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAN1A1 MUTATED       0                         0    15
  MAN1A1 WILD-TYPE     5                         1   269
D51V13, multiclass
                           clus
vv                          MAN1A1 MUTATED MAN1A1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 15              269
[1] 3 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
  MAN1A1 MUTATED     0  15
  MAN1A1 WILD-TYPE   3 268
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1A1 MUTATED      0   15
  MAN1A1 WILD-TYPE    3  268
                        clus
vv                       MAN1A1 MUTATED MAN1A1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             15              268
[1] 2 2
[1] FALSE

Clustering(52) Variable = OXA1L MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  OXA1L MUTATED    4  4
  OXA1L WILD-TYPE 93 99
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             192 
  OXA1L MUTATED OXA1L WILD-TYPE 
              4              99 
$`OXA1L MUTATED`
TCGA-EE-A180 TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A51T TCGA-DA-A1IA TCGA-EE-A181 
       31.96        27.35        36.85        11.34        64.83        20.38 
TCGA-EE-A2GB TCGA-EE-A2MS 
       26.14       143.93 

$`OXA1L WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
      134.40        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       42.05        45.70       177.86        15.02        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       60.10        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE 
      346.49       185.19       115.43        30.02        77.98        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       145.45       227.01        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  OXA1L MUTATED OXA1L WILD-TYPE 
          11.34            0.00 
  OXA1L MUTATED OXA1L WILD-TYPE 
         143.93          346.49 
  OXA1L MUTATED OXA1L WILD-TYPE 
         29.655          48.545 
[1] "11.3 - 143.9 (29.7)" "0.0 - 346.5 (48.5)" 
[1] "hr=" "1.5"
D52V2, survival
                 sevent
clus2               0   1
  OXA1L MUTATED     4   4
  OXA1L WILD-TYPE 120 156
  OXA1L MUTATED OXA1L WILD-TYPE 
              8             276 
  OXA1L MUTATED OXA1L WILD-TYPE 
              4             156 
$`OXA1L MUTATED`
TCGA-EE-A180 TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A51T TCGA-DA-A1IA TCGA-EE-A181 
       94.98        27.35        36.95        26.89        65.92        33.73 
TCGA-EE-A2GB TCGA-EE-A2MS 
       59.28       162.48 

$`OXA1L WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       62.07        46.32        13.87        68.25        54.02        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
      168.26         2.60       340.14       126.81       134.40        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        22.62        63.81       125.79       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 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
      176.55        35.93       135.02        88.87        53.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       78.97        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-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
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       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.29        86.14        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23        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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  OXA1L MUTATED OXA1L WILD-TYPE 
          26.89            0.20 
  OXA1L MUTATED OXA1L WILD-TYPE 
         162.48          369.93 
  OXA1L MUTATED OXA1L WILD-TYPE 
         48.115          53.970 
[1] "26.9 - 162.5 (48.1)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1"  
D52V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OXA1L MUTATED          0       0       0        0        0        2         0
  OXA1L WILD-TYPE       10       6      25       10       25       16        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OXA1L MUTATED           0         0         3          0          2
  OXA1L WILD-TYPE        14        10        33         14         24
                 vv
clus              STAGE IIIC STAGE IV
  OXA1L MUTATED            1        0
  OXA1L WILD-TYPE         42       16
D52V4, multiclass
            clus
vv           OXA1L MUTATED OXA1L WILD-TYPE
  I/II NOS               0              10
  STAGE 0                0               6
  STAGE I                0              25
  STAGE IA               0              10
  STAGE IB               0              25
  STAGE II               2              16
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              3              33
  STAGE IIIA             0              14
  STAGE IIIB             2              24
  STAGE IIIC             1              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
  OXA1L MUTATED       0  2  2  2
  OXA1L WILD-TYPE    53 60 58 53
D52V5, multiclass
       clus
vv      OXA1L MUTATED OXA1L WILD-TYPE
  T0+T1             0              53
  T2                2              60
  T3                2              58
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OXA1L MUTATED     3   3   2   0
  OXA1L WILD-TYPE 140  50  32  35
D52V6, multiclass
    clus
vv   OXA1L MUTATED OXA1L WILD-TYPE
  N0             3             140
  N1             3              50
  N2             2              32
  N3             0              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"
D52V7, binary
                 cls
clus                0   1
  OXA1L MUTATED     8   0
  OXA1L WILD-TYPE 248  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      8    0
  OXA1L WILD-TYPE  248   17
   clus
vv  OXA1L MUTATED OXA1L WILD-TYPE
  0             8             248
  1             0              17
[1] 2 2
[1] FALSE
D52V8, binary
                 cls
clus                0   1
  OXA1L MUTATED     3   2
  OXA1L WILD-TYPE 104  71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      3    2
  OXA1L WILD-TYPE  104   71
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  NO              3             104
  YES             2              71
[1] 2 2
[1] FALSE
D52V9, binary
                 cls
clus                0   1
  OXA1L MUTATED     1   7
  OXA1L WILD-TYPE  36 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      1    7
  OXA1L WILD-TYPE   36  246
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  NO              1              36
  YES             7             246
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, binary
                 cls
clus                0   1
  OXA1L MUTATED     3   5
  OXA1L WILD-TYPE 106 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      3    5
  OXA1L WILD-TYPE  106  176
        clus
vv       OXA1L MUTATED OXA1L WILD-TYPE
  FEMALE             3             106
  MALE               5             176
[1] 2 2
[1] FALSE
D52V12, binary
                 cls
clus                0   1
  OXA1L MUTATED     6   2
  OXA1L WILD-TYPE 248  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      6    2
  OXA1L WILD-TYPE  248   33
     clus
vv    OXA1L MUTATED OXA1L WILD-TYPE
  NO              6             248
  YES             2              33
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OXA1L MUTATED       0                         0     8
  OXA1L WILD-TYPE     5                         1   276
D52V13, multiclass
                           clus
vv                          OXA1L MUTATED OXA1L WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                 cls
clus                0   1
  OXA1L MUTATED     0   8
  OXA1L WILD-TYPE   3 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXA1L MUTATED      0    8
  OXA1L WILD-TYPE    3  275
                        clus
vv                       OXA1L MUTATED OXA1L WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             275
[1] 2 2
[1] FALSE

Clustering(53) Variable = NAP1L2 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2               0  1
  NAP1L2 MUTATED    9 11
  NAP1L2 WILD-TYPE 88 92
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
              20              180 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
              11               92 
$`NAP1L2 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JC TCGA-D3-A3C6 
       38.76        52.90        27.35        36.85        86.30        58.06 
TCGA-D3-A3MU TCGA-D9-A6EG TCGA-DA-A1HV TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F 
       23.67        22.85        76.34         0.00        75.55        79.20 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2GR TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MT 
       12.99        47.74         0.20        23.77        63.25        23.51 
TCGA-FS-A1Z3 TCGA-FS-A1ZZ 
        8.35         3.06 

$`NAP1L2 WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        33.24        31.96       166.75       269.03       134.40 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       62.86        15.75       168.00       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        66.08        43.53       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        90.21       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       15.02        22.29        69.21       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       24.89        20.38        26.24        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF 
       71.31        81.99       103.13        15.25         5.75       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       94.19       171.85        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.50       174.21       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
             0.0              0.2 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           86.30           346.49 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           32.10            49.53 
[1] "0.0 - 86.3 (32.1)"  "0.2 - 346.5 (49.5)"
[1] "hr=" "2"  
D53V2, survival
                  sevent
clus2                0   1
  NAP1L2 MUTATED    10  13
  NAP1L2 WILD-TYPE 114 147
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
              23              261 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
              13              147 
$`NAP1L2 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JC TCGA-D3-A2JD 
       46.32       126.81        27.35        36.95        86.76        11.87 
TCGA-D3-A3C6 TCGA-D3-A3MU TCGA-D9-A6EG TCGA-DA-A1HV TCGA-EE-A182 TCGA-EE-A20C 
       58.06        39.75        22.95        76.57        14.70       151.27 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2GR TCGA-EE-A2MC TCGA-EE-A2MJ 
       91.56        13.97        56.84        42.77        61.51        96.23 
TCGA-EE-A2MT TCGA-EE-A3JA TCGA-FS-A1Z3 TCGA-FS-A1ZZ TCGA-GF-A6C9 
       71.21        53.19        20.91        27.02        15.78 

$`NAP1L2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 
      168.26         2.60       340.14       134.40        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG 
      103.10        65.49        23.77       115.53       168.00       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        66.48        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        46.98       166.52        86.93        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        77.56        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       36.46        29.82        27.22         8.65        33.73        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.96       133.81        13.55        63.35        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12        13.91        81.21        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-A2MK 
      103.27       268.73       103.20        16.96       204.66       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      216.66       167.90        47.54       248.65        43.23       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        51.35       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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-A1ZG 
       27.72        48.85       357.37        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        19.43         2.04       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.35        10.42        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           11.87             0.20 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
          151.27           369.93 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           46.32            54.41 
[1] "11.9 - 151.3 (46.3)" "0.2 - 369.9 (54.4)" 
[1] "hr=" "1.4"
D53V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  NAP1L2 MUTATED          1       1       2        0        4        2
  NAP1L2 WILD-TYPE        9       5      23       10       21       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  NAP1L2 MUTATED           0         1         0         4          2
  NAP1L2 WILD-TYPE        10        13        10        32         12
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  NAP1L2 MUTATED            3          4        1
  NAP1L2 WILD-TYPE         23         39       15
D53V4, multiclass
            clus
vv           NAP1L2 MUTATED NAP1L2 WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 1                5
  STAGE I                 2               23
  STAGE IA                0               10
  STAGE IB                4               21
  STAGE II                2               16
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               4               32
  STAGE IIIA              2               12
  STAGE IIIB              3               23
  STAGE IIIC              4               39
  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
  NAP1L2 MUTATED       3  6  5  5
  NAP1L2 WILD-TYPE    50 56 55 50
D53V5, multiclass
       clus
vv      NAP1L2 MUTATED NAP1L2 WILD-TYPE
  T0+T1              3               50
  T2                 6               56
  T3                 5               55
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NAP1L2 MUTATED    13   5   5   1
  NAP1L2 WILD-TYPE 130  48  29  34
D53V6, multiclass
    clus
vv   NAP1L2 MUTATED NAP1L2 WILD-TYPE
  N0             13              130
  N1              5               48
  N2              5               29
  N3              1               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"
D53V7, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED    23   1
  NAP1L2 WILD-TYPE 233  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED     23    1
  NAP1L2 WILD-TYPE  233   16
   clus
vv  NAP1L2 MUTATED NAP1L2 WILD-TYPE
  0             23              233
  1              1               16
[1] 2 2
[1] FALSE
D53V8, binary
                  cls
clus                0  1
  NAP1L2 MUTATED    8  5
  NAP1L2 WILD-TYPE 99 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      8    5
  NAP1L2 WILD-TYPE   99   68
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO               8               99
  YES              5               68
[1] 2 2
[1] FALSE
D53V9, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     5  20
  NAP1L2 WILD-TYPE  32 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      5   20
  NAP1L2 WILD-TYPE   32  233
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO               5               32
  YES             20              233
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED    10  15
  NAP1L2 WILD-TYPE  99 166
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED     10   15
  NAP1L2 WILD-TYPE   99  166
        clus
vv       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  FEMALE             10               99
  MALE               15              166
[1] 2 2
[1] FALSE
D53V12, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED    20   5
  NAP1L2 WILD-TYPE 234  30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED     20    5
  NAP1L2 WILD-TYPE  234   30
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO              20              234
  YES              5               30
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAP1L2 MUTATED       0                         0    25
  NAP1L2 WILD-TYPE     5                         1   259
D53V13, multiclass
                           clus
vv                          NAP1L2 MUTATED NAP1L2 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 25              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"
D53V14, binary
                  cls
clus                 0   1
  NAP1L2 MUTATED     1  24
  NAP1L2 WILD-TYPE   2 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      1   24
  NAP1L2 WILD-TYPE    2  259
                        clus
vv                       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             24              259
[1] 2 2
[1] FALSE

Clustering(54) Variable = MPP7 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2             0  1
  MPP7 MUTATED   13 12
  MPP7 WILD-TYPE 84 91
  MPP7 MUTATED MPP7 WILD-TYPE 
            25            175 
  MPP7 MUTATED MPP7 WILD-TYPE 
            12             91 
$`MPP7 MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A2J8 
      134.40        27.35        19.04        36.85        76.41        62.86 
TCGA-D3-A2JH TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A20C 
       36.30        69.21        68.68        58.85         0.00        75.55 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GU TCGA-EE-A2MS TCGA-ER-A19N 
       76.14        12.99         0.26        81.99       143.93        42.51 
TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A4F9 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
       22.36         8.35        13.28        42.48       120.53        34.49 
TCGA-QB-A6FS 
        7.23 

$`MPP7 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       52.90         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
      133.25        19.04        62.60        25.64        45.99        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00        86.30       107.61       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 
       15.02        22.29        22.85        76.34       138.67       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        60.10        64.83        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
       20.38        26.24        79.20        75.22        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       71.31       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      227.01        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        59.84       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      146.63        73.05         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      174.21       171.78        49.74       195.98        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       18.51        66.67       173.19        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 
       96.92        17.06         7.59        46.92       297.01         0.20 
TCGA-RP-A693 
        0.33 

  MPP7 MUTATED MPP7 WILD-TYPE 
           0.0            0.2 
  MPP7 MUTATED MPP7 WILD-TYPE 
        143.93         346.49 
  MPP7 MUTATED MPP7 WILD-TYPE 
         42.48          47.74 
[1] "0.0 - 143.9 (42.5)" "0.2 - 346.5 (47.7)"
[1] "hr=" "1.3"
D54V2, survival
                sevent
clus2              0   1
  MPP7 MUTATED    16  16
  MPP7 WILD-TYPE 108 144
  MPP7 MUTATED MPP7 WILD-TYPE 
            32            252 
  MPP7 MUTATED MPP7 WILD-TYPE 
            16            144 
$`MPP7 MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A2J8 
      134.40        27.35        31.40        36.95        90.90        65.49 
TCGA-D3-A2JH TCGA-D3-A5GS TCGA-D9-A149 TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1IC 
       42.08        18.18        54.67        77.56       222.51        68.09 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       14.70       151.27        63.35        78.97        13.97        63.78 
TCGA-EE-A2GC TCGA-EE-A2GU TCGA-EE-A2MS TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N 
       67.43        94.82       162.48        26.37         6.44        44.09 
TCGA-ER-A2NC TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A4F9 TCGA-GN-A268 TCGA-GN-A4U3 
       43.82        20.91        48.85        34.03        62.79       121.91 
TCGA-GN-A4U4 TCGA-QB-A6FS 
       39.35         7.23 

$`MPP7 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A198 
       68.15       168.26         2.60       340.14       126.81        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        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-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 
      125.79       135.75       137.92       178.32       125.19       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       22.95        76.57        36.03       144.89        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        33.73        26.89         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       91.56        13.55        85.08        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
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       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.29        86.14        59.28       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       42.77        81.21        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       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23        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        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       13.02       302.07       152.35       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       50.89        49.48         8.88       148.18       105.07        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        27.72       357.37        53.52        46.45         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 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U7 
       96.92        10.13        64.44        32.48        48.00        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13       297.90         0.20         0.33         0.69 

  MPP7 MUTATED MPP7 WILD-TYPE 
          6.44           0.20 
  MPP7 MUTATED MPP7 WILD-TYPE 
        222.51         369.93 
  MPP7 MUTATED MPP7 WILD-TYPE 
         51.76          53.97 
[1] "6.4 - 222.5 (51.8)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1"  
D54V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MPP7 MUTATED          0       1       1        1        5        2         1
  MPP7 WILD-TYPE       10       5      24        9       20       16         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MPP7 MUTATED           3         0         4          2          2          4
  MPP7 WILD-TYPE        11        10        32         12         24         39
                vv
clus             STAGE IV
  MPP7 MUTATED          3
  MPP7 WILD-TYPE       13
D54V4, multiclass
            clus
vv           MPP7 MUTATED MPP7 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               1              5
  STAGE I               1             24
  STAGE IA              1              9
  STAGE IB              5             20
  STAGE II              2             16
  STAGE IIA             1              9
  STAGE IIB             3             11
  STAGE IIC             0             10
  STAGE III             4             32
  STAGE IIIA            2             12
  STAGE IIIB            2             24
  STAGE IIIC            4             39
  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  6 10  3
  MPP7 WILD-TYPE    48 56 50 52
D54V5, multiclass
       clus
vv      MPP7 MUTATED MPP7 WILD-TYPE
  T0+T1            5             48
  T2               6             56
  T3              10             50
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MPP7 MUTATED    15   8   4   3
  MPP7 WILD-TYPE 128  45  30  32
D54V6, multiclass
    clus
vv   MPP7 MUTATED MPP7 WILD-TYPE
  N0           15            128
  N1            8             45
  N2            4             30
  N3            3             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"
D54V7, binary
                cls
clus               0   1
  MPP7 MUTATED    28   3
  MPP7 WILD-TYPE 228  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED     28    3
  MPP7 WILD-TYPE  228   14
   clus
vv  MPP7 MUTATED MPP7 WILD-TYPE
  0           28            228
  1            3             14
[1] 2 2
[1] FALSE
D54V8, binary
                cls
clus              0  1
  MPP7 MUTATED   18  5
  MPP7 WILD-TYPE 89 68
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED     18    5
  MPP7 WILD-TYPE   89   68
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO            18             89
  YES            5             68
[1] 2 2
[1] FALSE
D54V9, binary
                cls
clus               0   1
  MPP7 MUTATED     6  26
  MPP7 WILD-TYPE  31 227
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      6   26
  MPP7 WILD-TYPE   31  227
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO             6             31
  YES           26            227
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, binary
                cls
clus               0   1
  MPP7 MUTATED     5  27
  MPP7 WILD-TYPE 104 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      5   27
  MPP7 WILD-TYPE  104  154
        clus
vv       MPP7 MUTATED MPP7 WILD-TYPE
  FEMALE            5            104
  MALE             27            154
[1] 2 2
[1] FALSE
D54V12, binary
                cls
clus               0   1
  MPP7 MUTATED    28   4
  MPP7 WILD-TYPE 226  31
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED     28    4
  MPP7 WILD-TYPE  226   31
     clus
vv    MPP7 MUTATED MPP7 WILD-TYPE
  NO            28            226
  YES            4             31
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MPP7 MUTATED       0                         0    32
  MPP7 WILD-TYPE     5                         1   252
D54V13, multiclass
                           clus
vv                          MPP7 MUTATED MPP7 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               32            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"
D54V14, binary
                cls
clus               0   1
  MPP7 MUTATED     0  31
  MPP7 WILD-TYPE   3 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP7 MUTATED      0   31
  MPP7 WILD-TYPE    3  252
                        clus
vv                       MPP7 MUTATED MPP7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           31            252
[1] 2 2
[1] FALSE

Clustering(55) Variable = BTK MUTATION ANALYSIS
D55V1, survival
               sevent
clus2            0  1
  BTK MUTATED    9  4
  BTK WILD-TYPE 88 99
  BTK MUTATED BTK WILD-TYPE 
           13           187 
  BTK MUTATED BTK WILD-TYPE 
            4            99 
$`BTK MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51T 
       62.07       134.40        64.83        66.08        90.21        11.34 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A2GM TCGA-EE-A3AE TCGA-ER-A19H 
       76.34       138.67        20.38        18.35        54.51       150.12 
TCGA-FS-A1Z3 
        8.35 

$`BTK WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       27.35        19.04        36.85         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      107.61        36.30       171.58        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        59.70        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       144.46        31.76        62.70        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I1 
      177.86        15.02        22.29        69.21        22.85        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        24.89         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       64.04         4.41         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.50       174.21       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  BTK MUTATED BTK WILD-TYPE 
         8.35          0.00 
  BTK MUTATED BTK WILD-TYPE 
       150.12        346.49 
  BTK MUTATED BTK WILD-TYPE 
        64.83         45.99 
[1] "8.3 - 150.1 (64.8)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.7"
D55V2, survival
               sevent
clus2             0   1
  BTK MUTATED    11   4
  BTK WILD-TYPE 113 156
  BTK MUTATED BTK WILD-TYPE 
           15           269 
  BTK MUTATED BTK WILD-TYPE 
            4           156 
$`BTK MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A51T 
       62.07       134.40        66.48        66.08       103.59        26.89 
TCGA-D9-A149 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-EE-A181 TCGA-EE-A2GM TCGA-EE-A3AE 
       54.67        76.57       144.89        33.73        75.48        54.51 
TCGA-ER-A19H TCGA-FS-A1Z3 TCGA-GF-A6C9 
      152.35        20.91        15.78 

$`BTK WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB 
      171.58        59.57       130.72        58.06        46.98       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        60.23        24.53         9.34        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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81       125.79       135.75       137.92       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 
        9.90        25.18        77.56        22.95        36.03        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
        7.04        36.46        29.82        27.22         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        13.81        41.59       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-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.51        19.30         9.90        19.43         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  BTK MUTATED BTK WILD-TYPE 
        15.78          0.20 
  BTK MUTATED BTK WILD-TYPE 
       152.35        369.93 
  BTK MUTATED BTK WILD-TYPE 
        66.08         53.19 
[1] "15.8 - 152.3 (66.1)" "0.2 - 369.9 (53.2)" 
[1] "hr=" "2.2"
D55V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  BTK MUTATED          0       0       1        2        0        1         0
  BTK WILD-TYPE       10       6      24        8       25       17        10
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BTK MUTATED           0         1         3          0          2          2
  BTK WILD-TYPE        14         9        33         14         24         41
               vv
clus            STAGE IV
  BTK MUTATED          1
  BTK WILD-TYPE       15
D55V4, multiclass
            clus
vv           BTK MUTATED BTK WILD-TYPE
  I/II NOS             0            10
  STAGE 0              0             6
  STAGE I              1            24
  STAGE IA             2             8
  STAGE IB             0            25
  STAGE II             1            17
  STAGE IIA            0            10
  STAGE IIB            0            14
  STAGE IIC            1             9
  STAGE III            3            33
  STAGE IIIA           0            14
  STAGE IIIB           2            24
  STAGE IIIC           2            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
  BTK MUTATED       5  2  1  2
  BTK WILD-TYPE    48 60 59 53
D55V5, multiclass
       clus
vv      BTK MUTATED BTK WILD-TYPE
  T0+T1           5            48
  T2              2            60
  T3              1            59
  T4              2            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  BTK MUTATED     7   5   1   1
  BTK WILD-TYPE 136  48  33  34
D55V6, multiclass
    clus
vv   BTK MUTATED BTK WILD-TYPE
  N0           7           136
  N1           5            48
  N2           1            33
  N3           1            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"
D55V7, binary
               cls
clus              0   1
  BTK MUTATED    13   1
  BTK WILD-TYPE 243  16
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED     13    1
  BTK WILD-TYPE  243   16
   clus
vv  BTK MUTATED BTK WILD-TYPE
  0          13           243
  1           1            16
[1] 2 2
[1] FALSE
D55V8, binary
               cls
clus              0   1
  BTK MUTATED     4   4
  BTK WILD-TYPE 103  69
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      4    4
  BTK WILD-TYPE  103   69
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO            4           103
  YES           4            69
[1] 2 2
[1] FALSE
D55V9, binary
               cls
clus              0   1
  BTK MUTATED     5  10
  BTK WILD-TYPE  32 243
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      5   10
  BTK WILD-TYPE   32  243
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO            5            32
  YES          10           243
[1] 2 2
[1] FALSE
D55V10, continuous
D55V11, binary
               cls
clus              0   1
  BTK MUTATED     9   6
  BTK WILD-TYPE 100 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      9    6
  BTK WILD-TYPE  100  175
        clus
vv       BTK MUTATED BTK WILD-TYPE
  FEMALE           9           100
  MALE             6           175
[1] 2 2
[1] FALSE
D55V12, binary
               cls
clus              0   1
  BTK MUTATED    11   4
  BTK WILD-TYPE 243  31
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED     11    4
  BTK WILD-TYPE  243   31
     clus
vv    BTK MUTATED BTK WILD-TYPE
  NO           11           243
  YES           4            31
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTK MUTATED       0                         0    15
  BTK WILD-TYPE     5                         1   269
D55V13, multiclass
                           clus
vv                          BTK MUTATED BTK WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              15           269
[1] 3 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
  BTK MUTATED     0  15
  BTK WILD-TYPE   3 268
[1] "tbl2"
               cls
clus            [,1] [,2]
  BTK MUTATED      0   15
  BTK WILD-TYPE    3  268
                        clus
vv                       BTK MUTATED BTK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          15           268
[1] 2 2
[1] FALSE

Clustering(56) Variable = SLC9A11 MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  SLC9A11 MUTATED   17 16
  SLC9A11 WILD-TYPE 80 87
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               33               167 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               16                87 
$`SLC9A11 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q8 
       52.90       134.40        27.35        19.04        36.85        19.04 
TCGA-D3-A51F TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A20C 
       30.67        58.85        42.64        13.15        24.89        75.55 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2A2 TCGA-EE-A2GB 
       79.20        12.99         0.26        47.41        30.02        26.14 
TCGA-EE-A2GR TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3JB 
        0.20        23.77        63.25       143.93        54.51       168.85 
TCGA-ER-A199 TCGA-ER-A19G TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZZ 
        7.82       184.60       120.76       171.78         8.35         3.06 
TCGA-FW-A3TV TCGA-GN-A262 TCGA-QB-A6FS 
       11.54        53.29         7.23 

$`SLC9A11 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       133.25 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       24.53         9.34        90.21        23.67       173.85       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 
       68.68       150.61       110.53        60.10        64.83        30.44 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A181 
      225.11         3.91        16.41        52.41        18.21        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29M 
        0.00        26.24        75.22        76.14        44.28        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       27.16        61.12       346.49       185.19       115.43        77.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.76        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75       209.79        94.19       171.85        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       64.04         4.41         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A 
        3.35        19.86       135.98        34.45        10.49         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81        11.47       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YY 
       15.48        32.05        74.47         4.50       174.21        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       23.21         5.29        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       80.68        55.59        19.30         9.90        18.25         1.91 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         0.20         0.33 

  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
              0.2               0.0 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
           184.60            346.49 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
            30.67             49.71 
[1] "0.2 - 184.6 (30.7)" "0.0 - 346.5 (49.7)"
[1] "hr=" "1.3"
D56V2, survival
                   sevent
clus2                 0   1
  SLC9A11 MUTATED    21  23
  SLC9A11 WILD-TYPE 103 137
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               44               240 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               23               137 
$`SLC9A11 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q8 
      126.81       134.40        27.35        31.40        36.95        28.08 
TCGA-D3-A2JK TCGA-D3-A51F TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A17X 
       12.10        55.73        35.93        68.09        43.36        29.82 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       27.22       151.27        91.56        13.97        63.78        64.64 
TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GR 
       61.28        59.64        59.28        67.43        48.72        42.77 
TCGA-EE-A2MC TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB 
       61.51        96.23       162.48        54.51        41.59       201.80 
TCGA-ER-A199 TCGA-ER-A19G TCGA-ER-A19P TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1Z3 
        9.17       302.07       162.08        15.72       216.92        20.91 
TCGA-FS-A1ZB TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FW-A3TV TCGA-GF-A6C9 TCGA-GN-A262 
       48.85        27.02        28.73        13.51        15.78       139.89 
TCGA-GN-A266 TCGA-QB-A6FS 
       10.13         7.23 

$`SLC9A11 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-ER-A198 TCGA-FS-A1ZF 
       68.15       168.26         2.60       340.14        50.76        15.45 
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-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51H 
        9.34       103.59        39.75        45.30       174.84        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       222.51       176.55       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       65.92        40.60        33.93        10.49       225.96        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29M 
       13.55        63.35        85.08        78.97        72.07        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        66.74        14.47       369.93        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       115.96        39.29        86.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      102.12        13.91        81.21        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73        64.04        28.77        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        53.19        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B 
      134.33       152.81        35.44        13.94        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        13.02        26.37       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        44.09        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1YY 
       12.95       149.03        92.98       174.21        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        28.08         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.09        77.82        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A5DY 
       26.73        54.41        80.68        17.46        55.59        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90        19.43         2.04       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13       297.90         0.20         0.33         0.69 

  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
             7.23              0.20 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
           302.07            369.93 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
           48.785            54.215 
[1] "7.2 - 302.1 (48.8)" "0.2 - 369.9 (54.2)"
[1] "hr=" "1"  
D56V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  SLC9A11 MUTATED          0       1       3        4        2        4
  SLC9A11 WILD-TYPE       10       5      22        6       23       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  SLC9A11 MUTATED           1         3         0         5          0
  SLC9A11 WILD-TYPE         9        11        10        31         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  SLC9A11 MUTATED            7          8        2
  SLC9A11 WILD-TYPE         19         35       14
D56V4, multiclass
            clus
vv           SLC9A11 MUTATED SLC9A11 WILD-TYPE
  I/II NOS                 0                10
  STAGE 0                  1                 5
  STAGE I                  3                22
  STAGE IA                 4                 6
  STAGE IB                 2                23
  STAGE II                 4                14
  STAGE IIA                1                 9
  STAGE IIB                3                11
  STAGE IIC                0                10
  STAGE III                5                31
  STAGE IIIA               0                14
  STAGE IIIB               7                19
  STAGE IIIC               8                35
  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
  SLC9A11 MUTATED      10  5 13  6
  SLC9A11 WILD-TYPE    43 57 47 49
D56V5, multiclass
       clus
vv      SLC9A11 MUTATED SLC9A11 WILD-TYPE
  T0+T1              10                43
  T2                  5                57
  T3                 13                47
  T4                  6                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC9A11 MUTATED    22   7   8   4
  SLC9A11 WILD-TYPE 121  46  26  31
D56V6, multiclass
    clus
vv   SLC9A11 MUTATED SLC9A11 WILD-TYPE
  N0              22               121
  N1               7                46
  N2               8                26
  N3               4                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"
D56V7, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    38   2
  SLC9A11 WILD-TYPE 218  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     38    2
  SLC9A11 WILD-TYPE  218   15
   clus
vv  SLC9A11 MUTATED SLC9A11 WILD-TYPE
  0              38               218
  1               2                15
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                 0  1
  SLC9A11 MUTATED   18 10
  SLC9A11 WILD-TYPE 89 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     18   10
  SLC9A11 WILD-TYPE   89   63
     clus
vv    SLC9A11 MUTATED SLC9A11 WILD-TYPE
  NO               18                89
  YES              10                63
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED     8  36
  SLC9A11 WILD-TYPE  29 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      8   36
  SLC9A11 WILD-TYPE   29  217
     clus
vv    SLC9A11 MUTATED SLC9A11 WILD-TYPE
  NO                8                29
  YES              36               217
[1] 2 2
[1] FALSE
D56V10, continuous
D56V11, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    13  31
  SLC9A11 WILD-TYPE  96 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     13   31
  SLC9A11 WILD-TYPE   96  150
        clus
vv       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  FEMALE              13                96
  MALE                31               150
[1] 2 2
[1] FALSE
D56V12, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    36   8
  SLC9A11 WILD-TYPE 218  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     36    8
  SLC9A11 WILD-TYPE  218   27
     clus
vv    SLC9A11 MUTATED SLC9A11 WILD-TYPE
  NO               36               218
  YES               8                27
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC9A11 MUTATED       1                         0    43
  SLC9A11 WILD-TYPE     4                         1   241
D56V13, multiclass
                           clus
vv                          SLC9A11 MUTATED SLC9A11 WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  43               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"
D56V14, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED     1  41
  SLC9A11 WILD-TYPE   2 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      1   41
  SLC9A11 WILD-TYPE    2  242
                        clus
vv                       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              41               242
[1] 2 2
[1] FALSE

Clustering(57) Variable = EMG1 MUTATION ANALYSIS
D57V1, survival
                sevent
clus2             0  1
  EMG1 MUTATED    1  4
  EMG1 WILD-TYPE 96 99
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            195 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4             99 
$`EMG1 MUTATED`
TCGA-D3-A3CB TCGA-EE-A20C TCGA-EE-A3J8 TCGA-ER-A19D TCGA-FS-A4FD 
      140.98        75.55         3.35        11.47        80.68 

$`EMG1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       66.08        43.53        58.06        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89       111.85        45.90       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
      173.19        13.28        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  EMG1 MUTATED EMG1 WILD-TYPE 
          3.35           0.00 
  EMG1 MUTATED EMG1 WILD-TYPE 
        140.98         346.49 
  EMG1 MUTATED EMG1 WILD-TYPE 
         75.55          47.18 
[1] "3.4 - 141.0 (75.5)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.8"
D57V2, survival
                sevent
clus2              0   1
  EMG1 MUTATED     1   6
  EMG1 WILD-TYPE 123 154
  EMG1 MUTATED EMG1 WILD-TYPE 
             7            277 
  EMG1 MUTATED EMG1 WILD-TYPE 
             6            154 
$`EMG1 MUTATED`
TCGA-FS-A1ZF TCGA-D3-A3CB TCGA-EE-A20C TCGA-EE-A29V TCGA-EE-A3J8 TCGA-ER-A19D 
       15.45       166.52       151.27        25.87        34.32        12.59 
TCGA-FS-A4FD 
       80.68 

$`EMG1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       27.35        31.40        50.76        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06        46.98        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       33.73        14.70        26.89         4.96       133.81        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        61.28       369.93       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        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       180.39       216.66       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 
       64.04        28.77        54.51        13.81        41.59       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-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        35.44        13.94         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       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         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-FW-A3I3 
       28.73       174.84        34.03        26.73        54.41        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  EMG1 MUTATED EMG1 WILD-TYPE 
         12.59           0.20 
  EMG1 MUTATED EMG1 WILD-TYPE 
        166.52         369.93 
  EMG1 MUTATED EMG1 WILD-TYPE 
         34.32          54.02 
[1] "12.6 - 166.5 (34.3)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1.8"
D57V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  EMG1 MUTATED          1       1       0        0        1        0         0
  EMG1 WILD-TYPE        9       5      25       10       24       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EMG1 MUTATED           0         1         0          1          0          2
  EMG1 WILD-TYPE        14         9        36         13         26         41
                vv
clus             STAGE IV
  EMG1 MUTATED          0
  EMG1 WILD-TYPE       16
D57V4, multiclass
            clus
vv           EMG1 MUTATED EMG1 WILD-TYPE
  I/II NOS              1              9
  STAGE 0               1              5
  STAGE I               0             25
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             0             14
  STAGE IIC             1              9
  STAGE III             0             36
  STAGE IIIA            1             13
  STAGE IIIB            0             26
  STAGE IIIC            2             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
  EMG1 MUTATED       0  3  1  2
  EMG1 WILD-TYPE    53 59 59 53
D57V5, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  T0+T1            0             53
  T2               3             59
  T3               1             59
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EMG1 MUTATED     4   2   0   1
  EMG1 WILD-TYPE 139  51  34  34
D57V6, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  N0            4            139
  N1            2             51
  N2            0             34
  N3            1             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"
D57V7, binary
                cls
clus               0   1
  EMG1 MUTATED     7   0
  EMG1 WILD-TYPE 249  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      7    0
  EMG1 WILD-TYPE  249   17
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            7            249
  1            0             17
[1] 2 2
[1] FALSE
D57V8, binary
                cls
clus               0   1
  EMG1 MUTATED     2   2
  EMG1 WILD-TYPE 105  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    2
  EMG1 WILD-TYPE  105   71
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             2            105
  YES            2             71
[1] 2 2
[1] FALSE
D57V9, binary
                cls
clus               0   1
  EMG1 MUTATED     0   7
  EMG1 WILD-TYPE  37 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    7
  EMG1 WILD-TYPE   37  246
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             0             37
  YES            7            246
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, binary
                cls
clus               0   1
  EMG1 MUTATED     2   5
  EMG1 WILD-TYPE 107 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    5
  EMG1 WILD-TYPE  107  176
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            2            107
  MALE              5            176
[1] 2 2
[1] FALSE
D57V12, binary
                cls
clus               0   1
  EMG1 MUTATED     7   0
  EMG1 WILD-TYPE 247  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      7    0
  EMG1 WILD-TYPE  247   35
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             7            247
  YES            0             35
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED       0                         0     7
  EMG1 WILD-TYPE     5                         1   277
D57V13, multiclass
                           clus
vv                          EMG1 MUTATED EMG1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                7            277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                cls
clus               0   1
  EMG1 MUTATED     0   7
  EMG1 WILD-TYPE   3 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    7
  EMG1 WILD-TYPE    3  276
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            7            276
[1] 2 2
[1] FALSE

Clustering(58) Variable = SELP MUTATION ANALYSIS
D58V1, survival
                sevent
clus2             0  1
  SELP MUTATED   11  9
  SELP WILD-TYPE 86 94
  SELP MUTATED SELP WILD-TYPE 
            20            180 
  SELP MUTATED SELP WILD-TYPE 
             9             94 
$`SELP MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q8 TCGA-D3-A2JO 
       62.07        52.90        19.04        36.85        19.04        66.08 
TCGA-D3-A3MU TCGA-DA-A1HV TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29D 
       23.67        76.34        24.89        20.38        75.55        12.99 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A2NG 
        0.26        47.74        26.14        64.04         6.28        28.67 
TCGA-FS-A1ZZ TCGA-FS-A4F0 
        3.06        18.51 

$`SELP WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       38.76        33.24        31.96       166.75       269.03       134.40 
TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       27.35         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        76.41        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       64.83        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        90.21       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        22.29        69.21        22.85       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       13.15         0.00        26.24        79.20        75.22        76.14 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        30.02        77.98        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
      122.73         4.41        54.51        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       10.19       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        5.29        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  SELP MUTATED SELP WILD-TYPE 
          0.26           0.00 
  SELP MUTATED SELP WILD-TYPE 
         76.34         346.49 
  SELP MUTATED SELP WILD-TYPE 
        25.515         49.725 
[1] "0.3 - 76.3 (25.5)"  "0.0 - 346.5 (49.7)"
[1] "hr=" "1.7"
D58V2, survival
                sevent
clus2              0   1
  SELP MUTATED    15  16
  SELP WILD-TYPE 109 144
  SELP MUTATED SELP WILD-TYPE 
            31            253 
  SELP MUTATED SELP WILD-TYPE 
            16            144 
$`SELP MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q8 TCGA-D3-A2JO 
       62.07       126.81        31.40        36.95        28.08        66.08 
TCGA-D3-A3C7 TCGA-D3-A3MU TCGA-D3-A5GU TCGA-DA-A1HV TCGA-EE-A17Y TCGA-EE-A181 
       46.98        39.75       125.19        76.57        27.22        33.73 
TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S 
      151.27        13.97        63.78        56.84        14.47        61.28 
TCGA-EE-A2GB TCGA-EE-A2MD TCGA-EE-A3AC TCGA-EE-A3AF TCGA-ER-A19E TCGA-ER-A2NG 
       59.28        47.28        64.04        13.81        13.02        48.99 
TCGA-FR-A69P TCGA-FS-A1ZA TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FC 
       15.72        27.72        27.02        77.82        28.73        54.41 
TCGA-GN-A266 
       10.13 

$`SELP WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 
      168.26         2.60       340.14       134.40        27.35        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        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        66.48        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        58.06       166.52        86.93        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       77.56        22.95        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       36.46        29.82         8.65        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       72.07        64.64        18.61        56.42        66.74       369.93 
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       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.29        86.14        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       180.39       216.66       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-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      124.31       122.73        28.77        54.51        41.59       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-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
        9.17        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        28.83        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      174.21       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        48.85       357.37        53.52        46.45 
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-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
       27.09        66.67       174.84        34.03        26.73        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2.04        15.78       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  SELP MUTATED SELP WILD-TYPE 
         10.13           0.20 
  SELP MUTATED SELP WILD-TYPE 
        151.27         369.93 
  SELP MUTATED SELP WILD-TYPE 
         46.98          54.67 
[1] "10.1 - 151.3 (47.0)" "0.2 - 369.9 (54.7)" 
[1] "hr=" "1.4"
D58V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SELP MUTATED          1       1       0        1        4        3         2
  SELP WILD-TYPE        9       5      25        9       21       15         8
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SELP MUTATED           3         0         3          1          5          6
  SELP WILD-TYPE        11        10        33         13         21         37
                vv
clus             STAGE IV
  SELP MUTATED          2
  SELP WILD-TYPE       14
D58V4, multiclass
            clus
vv           SELP MUTATED SELP WILD-TYPE
  I/II NOS              1              9
  STAGE 0               1              5
  STAGE I               0             25
  STAGE IA              1              9
  STAGE IB              4             21
  STAGE II              3             15
  STAGE IIA             2              8
  STAGE IIB             3             11
  STAGE IIC             0             10
  STAGE III             3             33
  STAGE IIIA            1             13
  STAGE IIIB            5             21
  STAGE IIIC            6             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
  SELP MUTATED       7  5 13  2
  SELP WILD-TYPE    46 57 47 53
D58V5, multiclass
       clus
vv      SELP MUTATED SELP WILD-TYPE
  T0+T1            7             46
  T2               5             57
  T3              13             47
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SELP MUTATED    15   6   5   5
  SELP WILD-TYPE 128  47  29  30
D58V6, multiclass
    clus
vv   SELP MUTATED SELP WILD-TYPE
  N0           15            128
  N1            6             47
  N2            5             29
  N3            5             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"
D58V7, binary
                cls
clus               0   1
  SELP MUTATED    29   2
  SELP WILD-TYPE 227  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     29    2
  SELP WILD-TYPE  227   15
   clus
vv  SELP MUTATED SELP WILD-TYPE
  0           29            227
  1            2             15
[1] 2 2
[1] FALSE
D58V8, binary
                cls
clus              0  1
  SELP MUTATED   12  9
  SELP WILD-TYPE 95 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     12    9
  SELP WILD-TYPE   95   64
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO            12             95
  YES            9             64
[1] 2 2
[1] FALSE
D58V9, binary
                cls
clus               0   1
  SELP MUTATED     7  26
  SELP WILD-TYPE  30 227
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      7   26
  SELP WILD-TYPE   30  227
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO             7             30
  YES           26            227
[1] 2 2
[1] FALSE
D58V10, continuous
D58V11, binary
                cls
clus               0   1
  SELP MUTATED    17  16
  SELP WILD-TYPE  92 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     17   16
  SELP WILD-TYPE   92  165
        clus
vv       SELP MUTATED SELP WILD-TYPE
  FEMALE           17             92
  MALE             16            165
[1] 2 2
[1] FALSE
D58V12, binary
                cls
clus               0   1
  SELP MUTATED    26   7
  SELP WILD-TYPE 228  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED     26    7
  SELP WILD-TYPE  228   28
     clus
vv    SELP MUTATED SELP WILD-TYPE
  NO            26            228
  YES            7             28
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SELP MUTATED       1                         0    32
  SELP WILD-TYPE     4                         1   252
D58V13, multiclass
                           clus
vv                          SELP MUTATED SELP WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               32            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"
D58V14, binary
                cls
clus               0   1
  SELP MUTATED     1  31
  SELP WILD-TYPE   2 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  SELP MUTATED      1   31
  SELP WILD-TYPE    2  252
                        clus
vv                       SELP MUTATED SELP WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           31            252
[1] 2 2
[1] FALSE

Clustering(59) Variable = PARM1 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  PARM1 MUTATED    4  8
  PARM1 WILD-TYPE 93 95
  PARM1 MUTATED PARM1 WILD-TYPE 
             12             188 
  PARM1 MUTATED PARM1 WILD-TYPE 
              8              95 
$`PARM1 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-EE-A182 
       38.76        27.35        36.85        49.35        62.86         0.00 
TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A3JI TCGA-ER-A2NC TCGA-FS-A1ZC TCGA-FS-A1ZM 
       12.99        27.16       135.98        22.36       312.07        78.61 

$`PARM1 WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
      134.40        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       45.70       177.86        15.02        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       26.24        75.55        79.20        75.22        76.14         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        47.74        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      120.76        49.71        47.18       146.63        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98         8.35        27.62        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       36.33       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  PARM1 MUTATED PARM1 WILD-TYPE 
            0.0             0.2 
  PARM1 MUTATED PARM1 WILD-TYPE 
         312.07          346.49 
  PARM1 MUTATED PARM1 WILD-TYPE 
         37.805          47.575 
[1] "0.0 - 312.1 (37.8)" "0.2 - 346.5 (47.6)"
[1] "hr=" "1.2"
D59V2, survival
                 sevent
clus2               0   1
  PARM1 MUTATED     6  13
  PARM1 WILD-TYPE 118 147
  PARM1 MUTATED PARM1 WILD-TYPE 
             19             265 
  PARM1 MUTATED PARM1 WILD-TYPE 
             13             147 
$`PARM1 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-EE-A182 
       46.32        27.35        36.95        71.80        65.49        14.70 
TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GI TCGA-EE-A3JI 
        4.96        13.97        56.42        25.87        48.72       152.81 
TCGA-ER-A2NC TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-GF-A6C9 
       43.82        27.72       357.37       101.26        74.73        15.78 
TCGA-GN-A266 
       10.13 

$`PARM1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
      168.26         2.60       340.14       126.81       134.40        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B 
       29.82        27.22         8.65        33.73        26.89       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        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       63.78        72.07        64.64        56.84        18.61        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        61.28       369.93       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       134.33        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       50.89        49.48         8.88       148.18       105.07        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       28.08         7.79        48.85        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38        23.93       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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.43         2.04       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  PARM1 MUTATED PARM1 WILD-TYPE 
           4.96            0.20 
  PARM1 MUTATED PARM1 WILD-TYPE 
         357.37          369.93 
  PARM1 MUTATED PARM1 WILD-TYPE 
          43.82           54.51 
[1] "5.0 - 357.4 (43.8)" "0.2 - 369.9 (54.5)"
[1] "hr=" "1.4"
D59V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PARM1 MUTATED          1       0       1        1        2        1         0
  PARM1 WILD-TYPE        9       6      24        9       23       17        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PARM1 MUTATED           0         1         4          0          2
  PARM1 WILD-TYPE        14         9        32         14         24
                 vv
clus              STAGE IIIC STAGE IV
  PARM1 MUTATED            5        0
  PARM1 WILD-TYPE         38       16
D59V4, multiclass
            clus
vv           PARM1 MUTATED PARM1 WILD-TYPE
  I/II NOS               1               9
  STAGE 0                0               6
  STAGE I                1              24
  STAGE IA               1               9
  STAGE IB               2              23
  STAGE II               1              17
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              1               9
  STAGE III              4              32
  STAGE IIIA             0              14
  STAGE IIIB             2              24
  STAGE IIIC             5              38
  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    52 58 57 50
D59V5, multiclass
       clus
vv      PARM1 MUTATED PARM1 WILD-TYPE
  T0+T1             1              52
  T2                4              58
  T3                3              57
  T4                5              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PARM1 MUTATED     7   4   4   2
  PARM1 WILD-TYPE 136  49  30  33
D59V6, multiclass
    clus
vv   PARM1 MUTATED PARM1 WILD-TYPE
  N0             7             136
  N1             4              49
  N2             4              30
  N3             2              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"
D59V7, binary
                 cls
clus                0   1
  PARM1 MUTATED    17   0
  PARM1 WILD-TYPE 239  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED     17    0
  PARM1 WILD-TYPE  239   17
   clus
vv  PARM1 MUTATED PARM1 WILD-TYPE
  0            17             239
  1             0              17
[1] 2 2
[1] FALSE
D59V8, binary
                 cls
clus                0   1
  PARM1 MUTATED     4   6
  PARM1 WILD-TYPE 103  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      4    6
  PARM1 WILD-TYPE  103   67
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  NO              4             103
  YES             6              67
[1] 2 2
[1] FALSE
D59V9, binary
                 cls
clus                0   1
  PARM1 MUTATED     3  16
  PARM1 WILD-TYPE  34 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      3   16
  PARM1 WILD-TYPE   34  237
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  NO              3              34
  YES            16             237
[1] 2 2
[1] FALSE
D59V10, continuous
D59V11, binary
                 cls
clus                0   1
  PARM1 MUTATED     5  14
  PARM1 WILD-TYPE 104 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      5   14
  PARM1 WILD-TYPE  104  167
        clus
vv       PARM1 MUTATED PARM1 WILD-TYPE
  FEMALE             5             104
  MALE              14             167
[1] 2 2
[1] FALSE
D59V12, binary
                 cls
clus                0   1
  PARM1 MUTATED    15   4
  PARM1 WILD-TYPE 239  31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED     15    4
  PARM1 WILD-TYPE  239   31
     clus
vv    PARM1 MUTATED PARM1 WILD-TYPE
  NO             15             239
  YES             4              31
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARM1 MUTATED       0                         0    19
  PARM1 WILD-TYPE     5                         1   265
D59V13, multiclass
                           clus
vv                          PARM1 MUTATED PARM1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                19             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"
D59V14, binary
                 cls
clus                0   1
  PARM1 MUTATED     0  19
  PARM1 WILD-TYPE   3 264
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARM1 MUTATED      0   19
  PARM1 WILD-TYPE    3  264
                        clus
vv                       PARM1 MUTATED PARM1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            19             264
[1] 2 2
[1] FALSE

Clustering(60) Variable = ACSBG1 MUTATION ANALYSIS
D60V1, survival
                  sevent
clus2                0   1
  ACSBG1 MUTATED     7   2
  ACSBG1 WILD-TYPE  90 101
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               9              191 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               2              101 
$`ACSBG1 MUTATED`
TCGA-EB-A5SG TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-DA-A1HY TCGA-EE-A29M 
       33.24        52.90       134.40        36.85       138.67        47.74 
TCGA-EE-A2GL TCGA-EE-A2MF TCGA-EE-A2MG 
       32.48       209.79        94.19 

$`ACSBG1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A3JD 
       62.07        38.76        31.96       166.75       269.03        27.35 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       42.05        45.70       177.86        15.02        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.85        76.34        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        44.28        47.41        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN 
       12.95       201.60        68.65        10.62        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75        23.77       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           32.48             0.00 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
          209.79           346.49 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           52.90            46.92 
[1] "32.5 - 209.8 (52.9)" "0.0 - 346.5 (46.9)" 
[1] "hr=" "3"  
D60V2, survival
                  sevent
clus2                0   1
  ACSBG1 MUTATED     7   5
  ACSBG1 WILD-TYPE 117 155
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
              12              272 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
               5              155 
$`ACSBG1 MUTATED`
TCGA-EB-A5SG TCGA-EE-A2GO TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-DA-A1HY TCGA-EE-A29M 
       68.25       126.81       134.40        36.95       144.89        56.84 
TCGA-EE-A2A0 TCGA-EE-A2GL TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A3AG TCGA-GN-A266 
       46.82        79.66       268.73       103.20        41.59        10.13 

$`ACSBG1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        13.87        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
      168.26         2.60       340.14        27.35        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       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 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
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-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        13.97        63.78        72.07        64.64 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87       195.02        17.92       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51        47.28       103.27        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       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 
       64.04        28.77        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-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
           10.13             0.20 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
          268.73           369.93 
  ACSBG1 MUTATED ACSBG1 WILD-TYPE 
          73.955           53.390 
[1] "10.1 - 268.7 (74.0)" "0.2 - 369.9 (53.4)" 
[1] "hr=" "1.7"
D60V3, continuous
                  vv
clus               I/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      22       10       24       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ACSBG1 MUTATED           2         0         0         3          0
  ACSBG1 WILD-TYPE         8        14        10        33         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ACSBG1 MUTATED            0          0        1
  ACSBG1 WILD-TYPE         26         43       15
D60V4, multiclass
            clus
vv           ACSBG1 MUTATED ACSBG1 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 3               22
  STAGE IA                0               10
  STAGE IB                1               24
  STAGE II                1               17
  STAGE IIA               2                8
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               3               33
  STAGE IIIA              0               14
  STAGE IIIB              0               26
  STAGE IIIC              0               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
  ACSBG1 MUTATED       1  5  3  0
  ACSBG1 WILD-TYPE    52 57 57 55
D60V5, multiclass
       clus
vv      ACSBG1 MUTATED ACSBG1 WILD-TYPE
  T0+T1              1               52
  T2                 5               57
  T3                 3               57
  T4                 0               55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ACSBG1 MUTATED     7   1   2   0
  ACSBG1 WILD-TYPE 136  52  32  35
D60V6, multiclass
    clus
vv   ACSBG1 MUTATED ACSBG1 WILD-TYPE
  N0              7              136
  N1              1               52
  N2              2               32
  N3              0               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"
D60V7, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED    10   1
  ACSBG1 WILD-TYPE 246  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED     10    1
  ACSBG1 WILD-TYPE  246   16
   clus
vv  ACSBG1 MUTATED ACSBG1 WILD-TYPE
  0             10              246
  1              1               16
[1] 2 2
[1] FALSE
D60V8, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     6   1
  ACSBG1 WILD-TYPE 101  72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      6    1
  ACSBG1 WILD-TYPE  101   72
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  NO               6              101
  YES              1               72
[1] 2 2
[1] FALSE
D60V9, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     2  11
  ACSBG1 WILD-TYPE  35 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      2   11
  ACSBG1 WILD-TYPE   35  242
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  NO               2               35
  YES             11              242
[1] 2 2
[1] FALSE
D60V10, continuous
D60V11, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED     6   7
  ACSBG1 WILD-TYPE 103 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      6    7
  ACSBG1 WILD-TYPE  103  174
        clus
vv       ACSBG1 MUTATED ACSBG1 WILD-TYPE
  FEMALE              6              103
  MALE                7              174
[1] 2 2
[1] FALSE
D60V12, binary
                  cls
clus                 0   1
  ACSBG1 MUTATED    11   2
  ACSBG1 WILD-TYPE 243  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED     11    2
  ACSBG1 WILD-TYPE  243   33
     clus
vv    ACSBG1 MUTATED ACSBG1 WILD-TYPE
  NO              11              243
  YES              2               33
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSBG1 MUTATED       0                         0    13
  ACSBG1 WILD-TYPE     5                         1   271
D60V13, multiclass
                           clus
vv                          ACSBG1 MUTATED ACSBG1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 13              271
[1] 3 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
  ACSBG1 MUTATED     0  13
  ACSBG1 WILD-TYPE   3 270
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSBG1 MUTATED      0   13
  ACSBG1 WILD-TYPE    3  270
                        clus
vv                       ACSBG1 MUTATED ACSBG1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             13              270
[1] 2 2
[1] FALSE

Clustering(61) Variable = CCK MUTATION ANALYSIS
D61V1, survival
               sevent
clus2             0   1
  CCK MUTATED     4   1
  CCK WILD-TYPE  93 102
  CCK MUTATED CCK WILD-TYPE 
            5           195 
  CCK MUTATED CCK WILD-TYPE 
            1           102 
$`CCK MUTATED`
TCGA-EE-A29E TCGA-EE-A2GJ TCGA-EE-A3JB TCGA-FS-A1ZT TCGA-GN-A265 
        0.26        68.65       168.85        35.28        96.92 

$`CCK WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
      177.86        15.02        22.29        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      201.60        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89       111.85        45.90         3.35        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        9.90        18.25         1.91        53.29       117.93        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  CCK MUTATED CCK WILD-TYPE 
         0.26          0.00 
  CCK MUTATED CCK WILD-TYPE 
       168.85        346.49 
  CCK MUTATED CCK WILD-TYPE 
        68.65         47.18 
[1] "0.3 - 168.8 (68.7)" "0.0 - 346.5 (47.2)"
[1] "hr=" "2.8"
D61V2, survival
               sevent
clus2             0   1
  CCK MUTATED     5   1
  CCK WILD-TYPE 119 159
  CCK MUTATED CCK WILD-TYPE 
            6           278 
  CCK MUTATED CCK WILD-TYPE 
            1           159 
$`CCK MUTATED`
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2GJ TCGA-EE-A3JB TCGA-FS-A1ZT TCGA-GN-A265 
       63.78        14.47       107.38       201.80        53.16        96.92 

$`CCK WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       78.97        13.97        72.07        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.42        66.74        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       59.28        67.43       173.79       220.24        48.72        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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        64.04        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
       19.43         2.04        15.78       139.89       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CCK MUTATED CCK WILD-TYPE 
        14.47          0.20 
  CCK MUTATED CCK WILD-TYPE 
       201.80        369.93 
  CCK MUTATED CCK WILD-TYPE 
        80.35         53.72 
[1] "14.5 - 201.8 (80.3)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "4"  
D61V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CCK MUTATED          0       0       0        1        0        0         0
  CCK WILD-TYPE       10       6      25        9       25       18        10
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CCK MUTATED           0         0         2          0          1          1
  CCK WILD-TYPE        14        10        34         14         25         42
               vv
clus            STAGE IV
  CCK MUTATED          0
  CCK WILD-TYPE       16
D61V4, multiclass
            clus
vv           CCK MUTATED CCK WILD-TYPE
  I/II NOS             0            10
  STAGE 0              0             6
  STAGE I              0            25
  STAGE IA             1             9
  STAGE IB             0            25
  STAGE II             0            18
  STAGE IIA            0            10
  STAGE IIB            0            14
  STAGE IIC            0            10
  STAGE III            2            34
  STAGE IIIA           0            14
  STAGE IIIB           1            25
  STAGE IIIC           1            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
  CCK MUTATED       1  1  3  0
  CCK WILD-TYPE    52 61 57 55
D61V5, multiclass
       clus
vv      CCK MUTATED CCK WILD-TYPE
  T0+T1           1            52
  T2              1            61
  T3              3            57
  T4              0            55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CCK MUTATED     1   4   0   0
  CCK WILD-TYPE 142  49  34  35
D61V6, multiclass
    clus
vv   CCK MUTATED CCK WILD-TYPE
  N0           1           142
  N1           4            49
  N2           0            34
  N3           0            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"
D61V7, binary
               cls
clus              0   1
  CCK MUTATED     5   0
  CCK WILD-TYPE 251  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      5    0
  CCK WILD-TYPE  251   17
   clus
vv  CCK MUTATED CCK WILD-TYPE
  0           5           251
  1           0            17
[1] 2 2
[1] FALSE
D61V8, binary
               cls
clus              0   1
  CCK MUTATED     2   1
  CCK WILD-TYPE 105  72
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      2    1
  CCK WILD-TYPE  105   72
     clus
vv    CCK MUTATED CCK WILD-TYPE
  NO            2           105
  YES           1            72
[1] 2 2
[1] FALSE
D61V9, binary
               cls
clus              0   1
  CCK MUTATED     1   5
  CCK WILD-TYPE  36 248
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      1    5
  CCK WILD-TYPE   36  248
     clus
vv    CCK MUTATED CCK WILD-TYPE
  NO            1            36
  YES           5           248
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, binary
               cls
clus              0   1
  CCK MUTATED     2   4
  CCK WILD-TYPE 107 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      2    4
  CCK WILD-TYPE  107  177
        clus
vv       CCK MUTATED CCK WILD-TYPE
  FEMALE           2           107
  MALE             4           177
[1] 2 2
[1] FALSE
D61V12, binary
               cls
clus              0   1
  CCK MUTATED     6   0
  CCK WILD-TYPE 248  35
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      6    0
  CCK WILD-TYPE  248   35
     clus
vv    CCK MUTATED CCK WILD-TYPE
  NO            6           248
  YES           0            35
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCK MUTATED       0                         0     6
  CCK WILD-TYPE     5                         1   278
D61V13, multiclass
                           clus
vv                          CCK MUTATED CCK WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               6           278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
               cls
clus              0   1
  CCK MUTATED     0   6
  CCK WILD-TYPE   3 277
[1] "tbl2"
               cls
clus            [,1] [,2]
  CCK MUTATED      0    6
  CCK WILD-TYPE    3  277
                        clus
vv                       CCK MUTATED CCK WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           6           277
[1] 2 2
[1] FALSE

Clustering(62) Variable = C1QTNF9 MUTATION ANALYSIS
D62V1, survival
                   sevent
clus2                 0   1
  C1QTNF9 MUTATED     9   3
  C1QTNF9 WILD-TYPE  88 100
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               12               188 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                3               100 
$`C1QTNF9 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-D3-A1QB TCGA-D9-A3Z1 TCGA-EE-A29M TCGA-EE-A2A1 
       62.07       134.40        62.60        15.02        47.74       115.43 
TCGA-EE-A2GM TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-FS-A4F9 
       18.35       171.85        53.26        67.89        45.90        13.28 

$`C1QTNF9 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       27.35        19.04        36.85         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J6 
      110.93        49.35       133.25        19.04        76.41        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC 
       11.34        42.05        45.70       177.86        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       76.14        12.99         0.26        44.28        47.41        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       346.49       185.19        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
       12.95       201.60        68.65        10.62        32.48        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK 
        5.75        23.77       209.79        94.19        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      104.78       145.45       227.01       143.93        23.51       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      122.73        64.04         4.41        54.51         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            13.28              0.00 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           171.85            346.49 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           57.665            46.455 
[1] "13.3 - 171.8 (57.7)" "0.0 - 346.5 (46.5)" 
[1] "hr=" "2"  
D62V2, survival
                   sevent
clus2                 0   1
  C1QTNF9 MUTATED    10   6
  C1QTNF9 WILD-TYPE 114 154
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
               16               268 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                6               154 
$`C1QTNF9 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-D3-A1QB TCGA-D3-A51N TCGA-D9-A3Z1 TCGA-EE-A29A 
       62.07       134.40        95.74        22.62        15.39        63.35 
TCGA-EE-A29M TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MU 
       56.84       115.96        75.48        47.28       204.66        53.26 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-FS-A4F9 
      172.18        64.08        53.19        34.03 

$`C1QTNF9 WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        63.81        26.89       125.79       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-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        7.10        22.29         9.90        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
        4.96       133.81       151.27        91.56        13.55        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       78.97        13.97        63.78        72.07        64.64        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66       102.12        13.91        42.77        81.21 
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-A2MJ 
       61.51       103.27       268.73       103.20        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      180.39       216.66       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        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        41.59       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       34.32       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            15.39              0.20 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
           204.66            369.93 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            62.71             53.34 
[1] "15.4 - 204.7 (62.7)" "0.2 - 369.9 (53.3)" 
[1] "hr=" "1.7"
D62V3, continuous
                   vv
clus                I/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      23        8       21       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C1QTNF9 MUTATED           0         1         1         1          1
  C1QTNF9 WILD-TYPE        10        13         9        35         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C1QTNF9 MUTATED            0          2        1
  C1QTNF9 WILD-TYPE         26         41       15
D62V4, multiclass
            clus
vv           C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  I/II NOS                 0                10
  STAGE 0                  0                 6
  STAGE I                  2                23
  STAGE IA                 2                 8
  STAGE IB                 4                21
  STAGE II                 1                17
  STAGE IIA                0                10
  STAGE IIB                1                13
  STAGE IIC                1                 9
  STAGE III                1                35
  STAGE IIIA               1                13
  STAGE IIIB               0                26
  STAGE IIIC               2                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
  C1QTNF9 MUTATED       4  7  2  3
  C1QTNF9 WILD-TYPE    49 55 58 52
D62V5, multiclass
       clus
vv      C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  T0+T1               4                49
  T2                  7                55
  T3                  2                58
  T4                  3                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C1QTNF9 MUTATED    11   1   1   3
  C1QTNF9 WILD-TYPE 132  52  33  32
D62V6, multiclass
    clus
vv   C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  N0              11               132
  N1               1                52
  N2               1                33
  N3               3                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"
D62V7, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED    15   1
  C1QTNF9 WILD-TYPE 241  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED     15    1
  C1QTNF9 WILD-TYPE  241   16
   clus
vv  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  0              15               241
  1               1                16
[1] 2 2
[1] FALSE
D62V8, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     7   4
  C1QTNF9 WILD-TYPE 100  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      7    4
  C1QTNF9 WILD-TYPE  100   69
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  NO                7               100
  YES               4                69
[1] 2 2
[1] FALSE
D62V9, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     2  14
  C1QTNF9 WILD-TYPE  35 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      2   14
  C1QTNF9 WILD-TYPE   35  239
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  NO                2                35
  YES              14               239
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     4  12
  C1QTNF9 WILD-TYPE 105 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      4   12
  C1QTNF9 WILD-TYPE  105  169
        clus
vv       C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  FEMALE               4               105
  MALE                12               169
[1] 2 2
[1] FALSE
D62V12, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED    15   1
  C1QTNF9 WILD-TYPE 239  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED     15    1
  C1QTNF9 WILD-TYPE  239   34
     clus
vv    C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  NO               15               239
  YES               1                34
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QTNF9 MUTATED       0                         0    16
  C1QTNF9 WILD-TYPE     5                         1   268
D62V13, multiclass
                           clus
vv                          C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               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"
D62V14, binary
                   cls
clus                  0   1
  C1QTNF9 MUTATED     0  15
  C1QTNF9 WILD-TYPE   3 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      0   15
  C1QTNF9 WILD-TYPE    3  268
                        clus
vv                       C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               268
[1] 2 2
[1] FALSE

Clustering(63) Variable = UBE2V2 MUTATION ANALYSIS
D63V1, survival
                  sevent
clus2                0   1
  UBE2V2 MUTATED     1   2
  UBE2V2 WILD-TYPE  96 101
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
               3              197 
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
               2              101 
$`UBE2V2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MI TCGA-EE-A2MJ 
       62.07       171.85        63.25 

$`UBE2V2 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      134.40        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75        23.77       209.79        94.19        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
           62.07             0.00 
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
          171.85           346.49 
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
           63.25            46.92 
[1] "62.1 - 171.8 (63.2)" "0.0 - 346.5 (46.9)" 
[1] "hr=" "1.1"
D63V2, survival
                  sevent
clus2                0   1
  UBE2V2 MUTATED     1   2
  UBE2V2 WILD-TYPE 123 158
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
               3              281 
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
               2              158 
$`UBE2V2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MI TCGA-EE-A2MJ 
       62.07       204.66        96.23 

$`UBE2V2 WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
           62.07             0.20 
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
          204.66           369.93 
  UBE2V2 MUTATED UBE2V2 WILD-TYPE 
           96.23            53.52 
[1] "62.1 - 204.7 (96.2)" "0.2 - 369.9 (53.5)" 
[1] "hr=" "1.4"
D63V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  UBE2V2 MUTATED          0       0       0        1        0        0
  UBE2V2 WILD-TYPE       10       6      25        9       25       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  UBE2V2 MUTATED           0         1         0         1          0
  UBE2V2 WILD-TYPE        10        13        10        35         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  UBE2V2 MUTATED            0          0        0
  UBE2V2 WILD-TYPE         26         43       16
D63V4, multiclass
            clus
vv           UBE2V2 MUTATED UBE2V2 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 0               25
  STAGE IA                1                9
  STAGE IB                0               25
  STAGE II                0               18
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               1               35
  STAGE IIIA              0               14
  STAGE IIIB              0               26
  STAGE IIIC              0               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
  UBE2V2 MUTATED       1  0  0  2
  UBE2V2 WILD-TYPE    52 62 60 53
D63V5, multiclass
       clus
vv      UBE2V2 MUTATED UBE2V2 WILD-TYPE
  T0+T1              1               52
  T2                 0               62
  T3                 0               60
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  UBE2V2 MUTATED     3   0   0   0
  UBE2V2 WILD-TYPE 140  53  34  35
D63V6, multiclass
    clus
vv   UBE2V2 MUTATED UBE2V2 WILD-TYPE
  N0              3              140
  N1              0               53
  N2              0               34
  N3              0               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"
D63V7, binary
                  cls
clus                 0   1
  UBE2V2 MUTATED     3   0
  UBE2V2 WILD-TYPE 253  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2V2 MUTATED      3    0
  UBE2V2 WILD-TYPE  253   17
   clus
vv  UBE2V2 MUTATED UBE2V2 WILD-TYPE
  0              3              253
  1              0               17
[1] 2 2
[1] FALSE
D63V8, binary
                  cls
clus                 0   1
  UBE2V2 MUTATED     2   0
  UBE2V2 WILD-TYPE 105  73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2V2 MUTATED      2    0
  UBE2V2 WILD-TYPE  105   73
     clus
vv    UBE2V2 MUTATED UBE2V2 WILD-TYPE
  NO               2              105
  YES              0               73
[1] 2 2
[1] FALSE
D63V9, binary
                  cls
clus                 0   1
  UBE2V2 MUTATED     0   3
  UBE2V2 WILD-TYPE  37 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2V2 MUTATED      0    3
  UBE2V2 WILD-TYPE   37  250
     clus
vv    UBE2V2 MUTATED UBE2V2 WILD-TYPE
  NO               0               37
  YES              3              250
[1] 2 2
[1] FALSE
D63V10, continuous
D63V11, binary
                  cls
clus                 0   1
  UBE2V2 MUTATED     0   3
  UBE2V2 WILD-TYPE 109 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2V2 MUTATED      0    3
  UBE2V2 WILD-TYPE  109  178
        clus
vv       UBE2V2 MUTATED UBE2V2 WILD-TYPE
  FEMALE              0              109
  MALE                3              178
[1] 2 2
[1] FALSE
D63V12, binary
                  cls
clus                 0   1
  UBE2V2 MUTATED     3   0
  UBE2V2 WILD-TYPE 251  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2V2 MUTATED      3    0
  UBE2V2 WILD-TYPE  251   35
     clus
vv    UBE2V2 MUTATED UBE2V2 WILD-TYPE
  NO               3              251
  YES              0               35
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBE2V2 MUTATED       0                         0     3
  UBE2V2 WILD-TYPE     5                         1   281
D63V13, multiclass
                           clus
vv                          UBE2V2 MUTATED UBE2V2 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  3              281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                  cls
clus                 0   1
  UBE2V2 MUTATED     0   3
  UBE2V2 WILD-TYPE   3 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2V2 MUTATED      0    3
  UBE2V2 WILD-TYPE    3  280
                        clus
vv                       UBE2V2 MUTATED UBE2V2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              280
[1] 2 2
[1] FALSE

Clustering(64) Variable = BOLA1 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  BOLA1 MUTATED     2   1
  BOLA1 WILD-TYPE  95 102
  BOLA1 MUTATED BOLA1 WILD-TYPE 
              3             197 
  BOLA1 MUTATED BOLA1 WILD-TYPE 
              1             102 
$`BOLA1 MUTATED`
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-EE-A3J7 
       15.02        22.29        45.90 

$`BOLA1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
      177.86        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89       111.85         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  BOLA1 MUTATED BOLA1 WILD-TYPE 
          15.02            0.00 
  BOLA1 MUTATED BOLA1 WILD-TYPE 
          45.90          346.49 
  BOLA1 MUTATED BOLA1 WILD-TYPE 
          22.29           47.74 
[1] "15.0 - 45.9 (22.3)" "0.0 - 346.5 (47.7)"
[1] "hr=" "1.5"
D64V2, survival
                 sevent
clus2               0   1
  BOLA1 MUTATED     2   1
  BOLA1 WILD-TYPE 122 159
  BOLA1 MUTATED BOLA1 WILD-TYPE 
              3             281 
  BOLA1 MUTATED BOLA1 WILD-TYPE 
              1             159 
$`BOLA1 MUTATED`
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-EE-A3J7 
       15.39        22.29        64.08 

$`BOLA1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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-A6E9 
      125.19       151.53        54.67         3.65         7.10         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       41.59       138.81       172.18       127.20        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       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  BOLA1 MUTATED BOLA1 WILD-TYPE 
          15.39            0.20 
  BOLA1 MUTATED BOLA1 WILD-TYPE 
          64.08          369.93 
  BOLA1 MUTATED BOLA1 WILD-TYPE 
          22.29           54.02 
[1] "15.4 - 64.1 (22.3)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.2"
D64V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  BOLA1 MUTATED          0       0       1        0        0        0         0
  BOLA1 WILD-TYPE       10       6      24       10       25       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BOLA1 MUTATED           0         0         0          0          1
  BOLA1 WILD-TYPE        14        10        36         14         25
                 vv
clus              STAGE IIIC STAGE IV
  BOLA1 MUTATED            1        0
  BOLA1 WILD-TYPE         42       16
D64V4, multiclass
            clus
vv           BOLA1 MUTATED BOLA1 WILD-TYPE
  I/II NOS               0              10
  STAGE 0                0               6
  STAGE I                1              24
  STAGE IA               0              10
  STAGE IB               0              25
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              0              36
  STAGE IIIA             0              14
  STAGE IIIB             1              25
  STAGE IIIC             1              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
  BOLA1 MUTATED       0  2  1  0
  BOLA1 WILD-TYPE    53 60 59 55
D64V5, multiclass
       clus
vv      BOLA1 MUTATED BOLA1 WILD-TYPE
  T0+T1             0              53
  T2                2              60
  T3                1              59
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BOLA1 MUTATED     1   1   0   1
  BOLA1 WILD-TYPE 142  52  34  34
D64V6, multiclass
    clus
vv   BOLA1 MUTATED BOLA1 WILD-TYPE
  N0             1             142
  N1             1              52
  N2             0              34
  N3             1              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"
D64V7, binary
                 cls
clus                0   1
  BOLA1 MUTATED     3   0
  BOLA1 WILD-TYPE 253  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BOLA1 MUTATED      3    0
  BOLA1 WILD-TYPE  253   17
   clus
vv  BOLA1 MUTATED BOLA1 WILD-TYPE
  0             3             253
  1             0              17
[1] 2 2
[1] FALSE
D64V8, binary
                 cls
clus                0   1
  BOLA1 MUTATED     1   1
  BOLA1 WILD-TYPE 106  72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BOLA1 MUTATED      1    1
  BOLA1 WILD-TYPE  106   72
     clus
vv    BOLA1 MUTATED BOLA1 WILD-TYPE
  NO              1             106
  YES             1              72
[1] 2 2
[1] FALSE
D64V9, binary
                 cls
clus                0   1
  BOLA1 MUTATED     0   3
  BOLA1 WILD-TYPE  37 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BOLA1 MUTATED      0    3
  BOLA1 WILD-TYPE   37  250
     clus
vv    BOLA1 MUTATED BOLA1 WILD-TYPE
  NO              0              37
  YES             3             250
[1] 2 2
[1] FALSE
D64V10, continuous
D64V11, binary
                 cls
clus                0   1
  BOLA1 MUTATED     1   2
  BOLA1 WILD-TYPE 108 179
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BOLA1 MUTATED      1    2
  BOLA1 WILD-TYPE  108  179
        clus
vv       BOLA1 MUTATED BOLA1 WILD-TYPE
  FEMALE             1             108
  MALE               2             179
[1] 2 2
[1] FALSE
D64V12, binary
                 cls
clus                0   1
  BOLA1 MUTATED     3   0
  BOLA1 WILD-TYPE 251  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BOLA1 MUTATED      3    0
  BOLA1 WILD-TYPE  251   35
     clus
vv    BOLA1 MUTATED BOLA1 WILD-TYPE
  NO              3             251
  YES             0              35
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BOLA1 MUTATED       0                         0     3
  BOLA1 WILD-TYPE     5                         1   281
D64V13, multiclass
                           clus
vv                          BOLA1 MUTATED BOLA1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 3             281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                 cls
clus                0   1
  BOLA1 MUTATED     0   3
  BOLA1 WILD-TYPE   3 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BOLA1 MUTATED      0    3
  BOLA1 WILD-TYPE    3  280
                        clus
vv                       BOLA1 MUTATED BOLA1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             280
[1] 2 2
[1] FALSE

Clustering(65) Variable = IFNGR2 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2                0   1
  IFNGR2 MUTATED     1   3
  IFNGR2 WILD-TYPE  96 100
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              196 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               3              100 
$`IFNGR2 MUTATED`
TCGA-EE-A180 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-EE-A29E 
       31.96        45.99        62.86         0.26 

$`IFNGR2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      134.40        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       62.60        25.64        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       75.22        76.14        12.99        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
            0.26             0.00 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
           62.86           346.49 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          38.975           47.575 
[1] "0.3 - 62.9 (39.0)"  "0.0 - 346.5 (47.6)"
[1] "hr=" "2.8"
D65V2, survival
                  sevent
clus2                0   1
  IFNGR2 MUTATED     1   3
  IFNGR2 WILD-TYPE 123 157
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               4              280 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               3              157 
$`IFNGR2 MUTATED`
TCGA-EE-A180 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-EE-A29E 
       94.98       103.10        65.49        63.78 

$`IFNGR2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       62.07        46.32        13.87        68.25        54.02        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90        95.74        43.43        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        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       180.39       216.66       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 
       64.04        28.77        54.51        13.81        41.59       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-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
           63.78             0.20 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          103.10           369.93 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          80.235           53.390 
[1] "63.8 - 103.1 (80.2)" "0.2 - 369.9 (53.4)" 
[1] "hr=" "1.2"
D65V3, continuous
                  vv
clus               I/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      25       10       24       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  IFNGR2 MUTATED           0         0         0         1          0
  IFNGR2 WILD-TYPE        10        14        10        35         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  IFNGR2 MUTATED            1          1        0
  IFNGR2 WILD-TYPE         25         42       16
D65V4, multiclass
            clus
vv           IFNGR2 MUTATED IFNGR2 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 0               25
  STAGE IA                0               10
  STAGE IB                1               24
  STAGE II                0               18
  STAGE IIA               0               10
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               1               35
  STAGE IIIA              0               14
  STAGE IIIB              1               25
  STAGE IIIC              1               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
  IFNGR2 MUTATED       0  1  2  1
  IFNGR2 WILD-TYPE    53 61 58 54
D65V5, multiclass
       clus
vv      IFNGR2 MUTATED IFNGR2 WILD-TYPE
  T0+T1              0               53
  T2                 1               61
  T3                 2               58
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  IFNGR2 MUTATED     2   2   0   0
  IFNGR2 WILD-TYPE 141  51  34  35
D65V6, multiclass
    clus
vv   IFNGR2 MUTATED IFNGR2 WILD-TYPE
  N0              2              141
  N1              2               51
  N2              0               34
  N3              0               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"
D65V7, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     4   0
  IFNGR2 WILD-TYPE 252  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      4    0
  IFNGR2 WILD-TYPE  252   17
   clus
vv  IFNGR2 MUTATED IFNGR2 WILD-TYPE
  0              4              252
  1              0               17
[1] 2 2
[1] FALSE
D65V8, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     3   1
  IFNGR2 WILD-TYPE 104  72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      3    1
  IFNGR2 WILD-TYPE  104   72
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               3              104
  YES              1               72
[1] 2 2
[1] FALSE
D65V9, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE  37 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE   37  249
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               0               37
  YES              4              249
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE 109 177
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE  109  177
        clus
vv       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  FEMALE              0              109
  MALE                4              177
[1] 2 2
[1] FALSE
D65V12, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     4   0
  IFNGR2 WILD-TYPE 250  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      4    0
  IFNGR2 WILD-TYPE  250   35
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               4              250
  YES              0               35
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFNGR2 MUTATED       0                         0     4
  IFNGR2 WILD-TYPE     5                         1   280
D65V13, multiclass
                           clus
vv                          IFNGR2 MUTATED IFNGR2 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  4              280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                  cls
clus                 0   1
  IFNGR2 MUTATED     0   4
  IFNGR2 WILD-TYPE   3 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    4
  IFNGR2 WILD-TYPE    3  279
                        clus
vv                       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              4              279
[1] 2 2
[1] FALSE

Clustering(66) Variable = KRAS MUTATION ANALYSIS
D66V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     2   2
  KRAS WILD-TYPE  95 101
  KRAS MUTATED KRAS WILD-TYPE 
             4            196 
  KRAS MUTATED KRAS WILD-TYPE 
             2            101 
$`KRAS MUTATED`
TCGA-D3-A51T TCGA-EE-A29B TCGA-EE-A2MT TCGA-FS-A1ZG 
       11.34        75.22        23.51         7.82 

$`KRAS WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      144.46        31.76        62.70        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      104.78       145.45       227.01       143.93        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       43.92        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  KRAS MUTATED KRAS WILD-TYPE 
          7.82           0.00 
  KRAS MUTATED KRAS WILD-TYPE 
         75.22         346.49 
  KRAS MUTATED KRAS WILD-TYPE 
        17.425         47.575 
[1] "7.8 - 75.2 (17.4)"  "0.0 - 346.5 (47.6)"
[1] "hr=" "2.1"
D66V2, survival
                sevent
clus2              0   1
  KRAS MUTATED     2   4
  KRAS WILD-TYPE 122 156
  KRAS MUTATED KRAS WILD-TYPE 
             6            278 
  KRAS MUTATED KRAS WILD-TYPE 
             4            156 
$`KRAS MUTATED`
TCGA-D3-A51T TCGA-EE-A29B TCGA-EE-A29N TCGA-EE-A2MT TCGA-FS-A1ZG TCGA-FS-A1ZK 
       26.89        85.08        18.61        71.21         9.70        23.93 

$`KRAS WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        56.84        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23       162.48        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       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-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        53.52        46.45        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        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  KRAS MUTATED KRAS WILD-TYPE 
           9.7            0.2 
  KRAS MUTATED KRAS WILD-TYPE 
         85.08         369.93 
  KRAS MUTATED KRAS WILD-TYPE 
        25.410         54.215 
[1] "9.7 - 85.1 (25.4)"  "0.2 - 369.9 (54.2)"
[1] "hr=" "2.2"
D66V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KRAS MUTATED          1       0       0        0        1        1         0
  KRAS WILD-TYPE        9       6      25       10       24       17        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KRAS MUTATED           1         0         0          0          0          2
  KRAS WILD-TYPE        13        10        36         14         26         41
                vv
clus             STAGE IV
  KRAS MUTATED          0
  KRAS WILD-TYPE       16
D66V4, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  I/II NOS              1              9
  STAGE 0               0              6
  STAGE I               0             25
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              1             17
  STAGE IIA             0             10
  STAGE IIB             1             13
  STAGE IIC             0             10
  STAGE III             0             36
  STAGE IIIA            0             14
  STAGE IIIB            0             26
  STAGE IIIC            2             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
  KRAS MUTATED       0  1  1  3
  KRAS WILD-TYPE    53 61 59 52
D66V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T0+T1            0             53
  T2               1             61
  T3               1             59
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KRAS MUTATED     4   1   1   0
  KRAS WILD-TYPE 139  52  33  35
D66V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0            4            139
  N1            1             52
  N2            1             33
  N3            0             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"
D66V7, binary
                cls
clus               0   1
  KRAS MUTATED     6   0
  KRAS WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      6    0
  KRAS WILD-TYPE  250   17
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            6            250
  1            0             17
[1] 2 2
[1] FALSE
D66V8, binary
                cls
clus               0   1
  KRAS MUTATED     1   3
  KRAS WILD-TYPE 106  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    3
  KRAS WILD-TYPE  106   70
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             1            106
  YES            3             70
[1] 2 2
[1] FALSE
D66V9, binary
                cls
clus               0   1
  KRAS MUTATED     0   6
  KRAS WILD-TYPE  37 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    6
  KRAS WILD-TYPE   37  247
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             0             37
  YES            6            247
[1] 2 2
[1] FALSE
D66V10, continuous
D66V11, binary
                cls
clus               0   1
  KRAS MUTATED     2   4
  KRAS WILD-TYPE 107 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    4
  KRAS WILD-TYPE  107  177
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            2            107
  MALE              4            177
[1] 2 2
[1] FALSE
D66V12, binary
                cls
clus               0   1
  KRAS MUTATED     4   2
  KRAS WILD-TYPE 250  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    2
  KRAS WILD-TYPE  250   33
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             4            250
  YES            2             33
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     6
  KRAS WILD-TYPE     5                         1   278
D66V13, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                6            278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                cls
clus               0   1
  KRAS MUTATED     0   6
  KRAS WILD-TYPE   3 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    6
  KRAS WILD-TYPE    3  277
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            6            277
[1] 2 2
[1] FALSE

Clustering(67) Variable = ZNF595 MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2                0   1
  ZNF595 MUTATED     5   1
  ZNF595 WILD-TYPE  92 102
  ZNF595 MUTATED ZNF595 WILD-TYPE 
               6              194 
  ZNF595 MUTATED ZNF595 WILD-TYPE 
               1              102 
$`ZNF595 MUTATED`
TCGA-EE-A2GO TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1HY TCGA-EE-A20C TCGA-EE-A2MS 
       52.90        11.34        69.21       138.67        75.55       143.93 

$`ZNF595 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      134.40        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       31.76        62.70        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.29        22.85        76.34        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        26.24        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       12.99         0.26        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  ZNF595 MUTATED ZNF595 WILD-TYPE 
           11.34             0.00 
  ZNF595 MUTATED ZNF595 WILD-TYPE 
          143.93           346.49 
  ZNF595 MUTATED ZNF595 WILD-TYPE 
          72.380           46.455 
[1] "11.3 - 143.9 (72.4)" "0.0 - 346.5 (46.5)" 
[1] "hr=" "3.6"
D67V2, survival
                  sevent
clus2                0   1
  ZNF595 MUTATED     7   1
  ZNF595 WILD-TYPE 117 159
  ZNF595 MUTATED ZNF595 WILD-TYPE 
               8              276 
  ZNF595 MUTATED ZNF595 WILD-TYPE 
               1              159 
$`ZNF595 MUTATED`
TCGA-EE-A2GO TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1HY TCGA-EE-A20C TCGA-EE-A2GC 
      126.81        26.89        77.56       144.89       151.27        67.43 
TCGA-EE-A2GI TCGA-EE-A2MS 
       48.72       162.48 

$`ZNF595 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A5GL 
       56.35       145.12        32.94        22.62        63.81       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        22.95        76.57        36.03        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       133.81        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       59.64        39.29        86.14        59.28       173.79       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23        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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  ZNF595 MUTATED ZNF595 WILD-TYPE 
           26.89             0.20 
  ZNF595 MUTATED ZNF595 WILD-TYPE 
          162.48           369.93 
  ZNF595 MUTATED ZNF595 WILD-TYPE 
         102.185           53.390 
[1] "26.9 - 162.5 (102.2)" "0.2 - 369.9 (53.4)"  
[1] "hr=" "5.9"
D67V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ZNF595 MUTATED          0       1       0        1        0        2
  ZNF595 WILD-TYPE       10       5      25        9       25       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ZNF595 MUTATED           0         1         0         1          1
  ZNF595 WILD-TYPE        10        13        10        35         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ZNF595 MUTATED            0          1        0
  ZNF595 WILD-TYPE         26         42       16
D67V4, multiclass
            clus
vv           ZNF595 MUTATED ZNF595 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 1                5
  STAGE I                 0               25
  STAGE IA                1                9
  STAGE IB                0               25
  STAGE II                2               16
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               1               35
  STAGE IIIA              1               13
  STAGE IIIB              0               26
  STAGE IIIC              1               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
  ZNF595 MUTATED       1  1  4  1
  ZNF595 WILD-TYPE    52 61 56 54
D67V5, multiclass
       clus
vv      ZNF595 MUTATED ZNF595 WILD-TYPE
  T0+T1              1               52
  T2                 1               61
  T3                 4               56
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF595 MUTATED     5   3   0   0
  ZNF595 WILD-TYPE 138  50  34  35
D67V6, multiclass
    clus
vv   ZNF595 MUTATED ZNF595 WILD-TYPE
  N0              5              138
  N1              3               50
  N2              0               34
  N3              0               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"
D67V7, binary
                  cls
clus                 0   1
  ZNF595 MUTATED     8   0
  ZNF595 WILD-TYPE 248  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF595 MUTATED      8    0
  ZNF595 WILD-TYPE  248   17
   clus
vv  ZNF595 MUTATED ZNF595 WILD-TYPE
  0              8              248
  1              0               17
[1] 2 2
[1] FALSE
D67V8, binary
                  cls
clus                 0   1
  ZNF595 MUTATED     4   3
  ZNF595 WILD-TYPE 103  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF595 MUTATED      4    3
  ZNF595 WILD-TYPE  103   70
     clus
vv    ZNF595 MUTATED ZNF595 WILD-TYPE
  NO               4              103
  YES              3               70
[1] 2 2
[1] FALSE
D67V9, binary
                  cls
clus                 0   1
  ZNF595 MUTATED     0   8
  ZNF595 WILD-TYPE  37 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF595 MUTATED      0    8
  ZNF595 WILD-TYPE   37  245
     clus
vv    ZNF595 MUTATED ZNF595 WILD-TYPE
  NO               0               37
  YES              8              245
[1] 2 2
[1] FALSE
D67V10, continuous
D67V11, binary
                  cls
clus                 0   1
  ZNF595 MUTATED     2   6
  ZNF595 WILD-TYPE 107 175
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF595 MUTATED      2    6
  ZNF595 WILD-TYPE  107  175
        clus
vv       ZNF595 MUTATED ZNF595 WILD-TYPE
  FEMALE              2              107
  MALE                6              175
[1] 2 2
[1] FALSE
D67V12, binary
                  cls
clus                 0   1
  ZNF595 MUTATED     7   1
  ZNF595 WILD-TYPE 247  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF595 MUTATED      7    1
  ZNF595 WILD-TYPE  247   34
     clus
vv    ZNF595 MUTATED ZNF595 WILD-TYPE
  NO               7              247
  YES              1               34
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF595 MUTATED       0                         0     8
  ZNF595 WILD-TYPE     5                         1   276
D67V13, multiclass
                           clus
vv                          ZNF595 MUTATED ZNF595 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  8              276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                  cls
clus                 0   1
  ZNF595 MUTATED     0   8
  ZNF595 WILD-TYPE   3 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF595 MUTATED      0    8
  ZNF595 WILD-TYPE    3  275
                        clus
vv                       ZNF595 MUTATED ZNF595 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              8              275
[1] 2 2
[1] FALSE

Clustering(68) Variable = PRKAA2 MUTATION ANALYSIS
D68V1, survival
                  sevent
clus2                0   1
  PRKAA2 MUTATED    17   3
  PRKAA2 WILD-TYPE  80 100
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              20              180 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
               3              100 
$`PRKAA2 MUTATED`
TCGA-EB-A5SG TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A2JH TCGA-D3-A51T TCGA-D9-A6EC 
       33.24       134.40        36.85        36.30        11.34        69.21 
TCGA-DA-A1I1 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29M TCGA-EE-A2GL 
       68.68        26.24        75.55        79.20        47.74        32.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19H 
       53.26       124.31        54.51        45.90         4.54       150.12 
TCGA-GN-A4U4 TCGA-GN-A4U8 
       34.49        46.92 

$`PRKAA2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        31.96       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       27.35        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
      173.85        30.67       144.46        31.76        62.70        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV 
       45.70       177.86        15.02        22.29        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
      138.67       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29B 
       18.21        13.15        24.89        20.38         0.00        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P 
       76.14        12.99         0.26        44.28        47.41        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM 
       26.14        12.95       201.60        68.65        10.62        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
       23.51       122.73        64.04         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      111.85         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       10.49         7.82        53.29        39.81        11.47       184.60 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.59       120.53       297.01         7.23         0.20         0.33 

  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
            4.54             0.00 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
          150.12           346.49 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
          47.330           47.295 
[1] "4.5 - 150.1 (47.3)" "0.0 - 346.5 (47.3)"
[1] "hr=" "3.2"
D68V2, survival
                  sevent
clus2                0   1
  PRKAA2 MUTATED    19   6
  PRKAA2 WILD-TYPE 105 154
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              25              259 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
               6              154 
$`PRKAA2 MUTATED`
TCGA-EB-A5SG TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A2JH TCGA-D3-A51T TCGA-D9-A1JW 
       68.25       134.40        36.95        42.08        26.89         3.65 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5UL TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       77.56       222.51        29.29        26.89       151.27        91.56 
TCGA-EE-A29M TCGA-EE-A2A0 TCGA-EE-A2GL TCGA-EE-A2M5 TCGA-EE-A2MU TCGA-EE-A3AA 
       56.84        46.82        79.66        21.67        53.26       124.31 
TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19H TCGA-GN-A266 TCGA-GN-A4U4 
       54.51        64.08        77.75       152.35        10.13        39.35 
TCGA-GN-A4U8 
       48.89 

$`PRKAA2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        13.87        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       86.76        11.87       113.52        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81       125.79       135.75       137.92       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29         9.90        25.18        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      144.89        20.38       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
      225.96        43.36        13.87        10.36        20.35        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       14.70         4.96       133.81        13.55        63.35        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       78.97        13.97        63.78        72.07        64.64        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
      195.02        17.92       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       43.23       162.48        71.21       122.73        64.04        28.77 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33       152.81 
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-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       302.07         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       96.92        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       10.42        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
            3.65             0.20 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
          222.51           369.93 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
           54.51            53.92 
[1] "3.6 - 222.5 (54.5)" "0.2 - 369.9 (53.9)"
[1] "hr=" "2.3"
D68V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PRKAA2 MUTATED          0       2       4        2        2        0
  PRKAA2 WILD-TYPE       10       4      21        8       23       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PRKAA2 MUTATED           3         0         0         4          1
  PRKAA2 WILD-TYPE         7        14        10        32         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PRKAA2 MUTATED            0          1        1
  PRKAA2 WILD-TYPE         26         42       15
D68V4, multiclass
            clus
vv           PRKAA2 MUTATED PRKAA2 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 2                4
  STAGE I                 4               21
  STAGE IA                2                8
  STAGE IB                2               23
  STAGE II                0               18
  STAGE IIA               3                7
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               4               32
  STAGE IIIA              1               13
  STAGE IIIB              0               26
  STAGE IIIC              1               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
  PRKAA2 MUTATED       7  5  3  1
  PRKAA2 WILD-TYPE    46 57 57 54
D68V5, multiclass
       clus
vv      PRKAA2 MUTATED PRKAA2 WILD-TYPE
  T0+T1              7               46
  T2                 5               57
  T3                 3               57
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PRKAA2 MUTATED    14   3   4   0
  PRKAA2 WILD-TYPE 129  50  30  35
D68V6, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  N0             14              129
  N1              3               50
  N2              4               30
  N3              0               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"
D68V7, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    21   1
  PRKAA2 WILD-TYPE 235  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     21    1
  PRKAA2 WILD-TYPE  235   16
   clus
vv  PRKAA2 MUTATED PRKAA2 WILD-TYPE
  0             21              235
  1              1               16
[1] 2 2
[1] FALSE
D68V8, binary
                  cls
clus                0  1
  PRKAA2 MUTATED   11  3
  PRKAA2 WILD-TYPE 96 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     11    3
  PRKAA2 WILD-TYPE   96   70
     clus
vv    PRKAA2 MUTATED PRKAA2 WILD-TYPE
  NO              11               96
  YES              3               70
[1] 2 2
[1] FALSE
D68V9, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED     4  21
  PRKAA2 WILD-TYPE  33 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED      4   21
  PRKAA2 WILD-TYPE   33  232
     clus
vv    PRKAA2 MUTATED PRKAA2 WILD-TYPE
  NO               4               33
  YES             21              232
[1] 2 2
[1] FALSE
D68V10, continuous
D68V11, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED     6  19
  PRKAA2 WILD-TYPE 103 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED      6   19
  PRKAA2 WILD-TYPE  103  162
        clus
vv       PRKAA2 MUTATED PRKAA2 WILD-TYPE
  FEMALE              6              103
  MALE               19              162
[1] 2 2
[1] FALSE
D68V12, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    19   6
  PRKAA2 WILD-TYPE 235  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     19    6
  PRKAA2 WILD-TYPE  235   29
     clus
vv    PRKAA2 MUTATED PRKAA2 WILD-TYPE
  NO              19              235
  YES              6               29
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKAA2 MUTATED       0                         0    25
  PRKAA2 WILD-TYPE     5                         1   259
D68V13, multiclass
                           clus
vv                          PRKAA2 MUTATED PRKAA2 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 25              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"
D68V14, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED     0  25
  PRKAA2 WILD-TYPE   3 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED      0   25
  PRKAA2 WILD-TYPE    3  258
                        clus
vv                       PRKAA2 MUTATED PRKAA2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             25              258
[1] 2 2
[1] FALSE

Clustering(69) Variable = MMP27 MUTATION ANALYSIS
D69V1, survival
                 sevent
clus2              0  1
  MMP27 MUTATED    3  6
  MMP27 WILD-TYPE 94 97
  MMP27 MUTATED MMP27 WILD-TYPE 
              9             191 
  MMP27 MUTATED MMP27 WILD-TYPE 
              6              97 
$`MMP27 MUTATED`
TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A3MU TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A29T 
       19.04        36.85        23.67        24.89         0.00       346.49 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
        0.20       171.85        63.25 

$`MMP27 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90       134.40        27.35         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       90.21       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       20.38        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       12.99         0.26        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       61.12       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.76        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75        23.77       209.79        94.19        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  MMP27 MUTATED MMP27 WILD-TYPE 
            0.0             0.2 
  MMP27 MUTATED MMP27 WILD-TYPE 
         346.49          312.07 
  MMP27 MUTATED MMP27 WILD-TYPE 
          24.89           47.74 
[1] "0.0 - 346.5 (24.9)" "0.2 - 312.1 (47.7)"
[1] "hr=" "1.1"
D69V2, survival
                 sevent
clus2               0   1
  MMP27 MUTATED     5   8
  MMP27 WILD-TYPE 119 152
  MMP27 MUTATED MMP27 WILD-TYPE 
             13             271 
  MMP27 MUTATED MMP27 WILD-TYPE 
              8             152 
$`MMP27 MUTATED`
TCGA-EE-A29L TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A3MU TCGA-EE-A17Y TCGA-EE-A182 
        2.60        31.40        36.95        39.75        27.22        14.70 
TCGA-EE-A29T TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-GF-A6C9 
      369.93        67.43        42.77       204.66        96.23        15.78 
TCGA-GN-A266 
       10.13 

$`MMP27 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26       340.14       126.81       134.40        27.35 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       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 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       36.46        29.82         8.65        33.73        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       78.97        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        66.74        14.47        61.28        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       54.74        79.66        75.48       102.12        13.91        81.21 
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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       19.43         2.04       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  MMP27 MUTATED MMP27 WILD-TYPE 
            2.6             0.2 
  MMP27 MUTATED MMP27 WILD-TYPE 
         369.93          357.37 
  MMP27 MUTATED MMP27 WILD-TYPE 
          36.95           54.51 
[1] "2.6 - 369.9 (37.0)" "0.2 - 357.4 (54.5)"
[1] "hr=" "1.1"
D69V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MMP27 MUTATED          0       0       0        0        0        1         0
  MMP27 WILD-TYPE       10       6      25       10       25       17        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MMP27 MUTATED           3         0         2          1          2
  MMP27 WILD-TYPE        11        10        34         13         24
                 vv
clus              STAGE IIIC STAGE IV
  MMP27 MUTATED            2        0
  MMP27 WILD-TYPE         41       16
D69V4, multiclass
            clus
vv           MMP27 MUTATED MMP27 WILD-TYPE
  I/II NOS               0              10
  STAGE 0                0               6
  STAGE I                0              25
  STAGE IA               0              10
  STAGE IB               0              25
  STAGE II               1              17
  STAGE IIA              0              10
  STAGE IIB              3              11
  STAGE IIC              0              10
  STAGE III              2              34
  STAGE IIIA             1              13
  STAGE IIIB             2              24
  STAGE IIIC             2              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
  MMP27 MUTATED       0  0  4  5
  MMP27 WILD-TYPE    53 62 56 50
D69V5, multiclass
       clus
vv      MMP27 MUTATED MMP27 WILD-TYPE
  T0+T1             0              53
  T2                0              62
  T3                4              56
  T4                5              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MMP27 MUTATED     5   2   2   1
  MMP27 WILD-TYPE 138  51  32  34
D69V6, multiclass
    clus
vv   MMP27 MUTATED MMP27 WILD-TYPE
  N0             5             138
  N1             2              51
  N2             2              32
  N3             1              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"
D69V7, binary
                 cls
clus                0   1
  MMP27 MUTATED    11   0
  MMP27 WILD-TYPE 245  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED     11    0
  MMP27 WILD-TYPE  245   17
   clus
vv  MMP27 MUTATED MMP27 WILD-TYPE
  0            11             245
  1             0              17
[1] 2 2
[1] FALSE
D69V8, binary
                 cls
clus                0   1
  MMP27 MUTATED     3   4
  MMP27 WILD-TYPE 104  69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      3    4
  MMP27 WILD-TYPE  104   69
     clus
vv    MMP27 MUTATED MMP27 WILD-TYPE
  NO              3             104
  YES             4              69
[1] 2 2
[1] FALSE
D69V9, binary
                 cls
clus                0   1
  MMP27 MUTATED     2  11
  MMP27 WILD-TYPE  35 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      2   11
  MMP27 WILD-TYPE   35  242
     clus
vv    MMP27 MUTATED MMP27 WILD-TYPE
  NO              2              35
  YES            11             242
[1] 2 2
[1] FALSE
D69V10, continuous
D69V11, binary
                 cls
clus                0   1
  MMP27 MUTATED     2  11
  MMP27 WILD-TYPE 107 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      2   11
  MMP27 WILD-TYPE  107  170
        clus
vv       MMP27 MUTATED MMP27 WILD-TYPE
  FEMALE             2             107
  MALE              11             170
[1] 2 2
[1] FALSE
D69V12, binary
                 cls
clus                0   1
  MMP27 MUTATED    11   2
  MMP27 WILD-TYPE 243  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED     11    2
  MMP27 WILD-TYPE  243   33
     clus
vv    MMP27 MUTATED MMP27 WILD-TYPE
  NO             11             243
  YES             2              33
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP27 MUTATED       1                         0    12
  MMP27 WILD-TYPE     4                         1   272
D69V13, multiclass
                           clus
vv                          MMP27 MUTATED MMP27 WILD-TYPE
  ASIAN                                 1               4
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                12             272
[1] 3 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
  MMP27 MUTATED     0  12
  MMP27 WILD-TYPE   3 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      0   12
  MMP27 WILD-TYPE    3  271
                        clus
vv                       MMP27 MUTATED MMP27 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            12             271
[1] 2 2
[1] FALSE

Clustering(70) Variable = POLR2B MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2                0   1
  POLR2B MUTATED     2   3
  POLR2B WILD-TYPE  95 100
  POLR2B MUTATED POLR2B WILD-TYPE 
               5              195 
  POLR2B MUTATED POLR2B WILD-TYPE 
               3              100 
$`POLR2B MUTATED`
TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-DA-A1HY TCGA-DA-A1IC TCGA-EE-A3AD 
       36.85       110.93       138.67        58.85         4.41 

$`POLR2B WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        27.35        19.04         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       31.89        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.29        69.21        22.85        76.34        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        60.10        64.83        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       64.04        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  POLR2B MUTATED POLR2B WILD-TYPE 
            4.41             0.00 
  POLR2B MUTATED POLR2B WILD-TYPE 
          138.67           346.49 
  POLR2B MUTATED POLR2B WILD-TYPE 
           58.85            47.18 
[1] "4.4 - 138.7 (58.9)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.2"
D70V2, survival
                  sevent
clus2                0   1
  POLR2B MUTATED     4   6
  POLR2B WILD-TYPE 120 154
  POLR2B MUTATED POLR2B WILD-TYPE 
              10              274 
  POLR2B MUTATED POLR2B WILD-TYPE 
               6              154 
$`POLR2B MUTATED`
TCGA-EE-A29L TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-D3-A2JD TCGA-D3-A5GO TCGA-DA-A1HY 
        2.60        36.95       112.57        11.87       137.92       144.89 
TCGA-DA-A1IC TCGA-EE-A2GC TCGA-EE-A3AD TCGA-FS-A1ZP 
       68.09        67.43        28.77        74.73 

$`POLR2B WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       86.76       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       22.62        63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       76.57        36.03        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
      135.02        88.87        53.92        65.92        40.60        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        64.04        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  POLR2B MUTATED POLR2B WILD-TYPE 
             2.6              0.2 
  POLR2B MUTATED POLR2B WILD-TYPE 
          144.89           369.93 
  POLR2B MUTATED POLR2B WILD-TYPE 
           67.76            53.72 
[1] "2.6 - 144.9 (67.8)" "0.2 - 369.9 (53.7)"
[1] "hr=" "1.2"
D70V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  POLR2B MUTATED          1       0       0        0        0        2
  POLR2B WILD-TYPE        9       6      25       10       25       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  POLR2B MUTATED           0         1         0         3          0
  POLR2B WILD-TYPE        10        13        10        33         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  POLR2B MUTATED            1          2        0
  POLR2B WILD-TYPE         25         41       16
D70V4, multiclass
            clus
vv           POLR2B MUTATED POLR2B WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 0                6
  STAGE I                 0               25
  STAGE IA                0               10
  STAGE IB                0               25
  STAGE II                2               16
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               3               33
  STAGE IIIA              0               14
  STAGE IIIB              1               25
  STAGE IIIC              2               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
  POLR2B MUTATED       1  1  3  3
  POLR2B WILD-TYPE    52 61 57 52
D70V5, multiclass
       clus
vv      POLR2B MUTATED POLR2B WILD-TYPE
  T0+T1              1               52
  T2                 1               61
  T3                 3               57
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  POLR2B MUTATED     4   3   2   1
  POLR2B WILD-TYPE 139  50  32  34
D70V6, multiclass
    clus
vv   POLR2B MUTATED POLR2B WILD-TYPE
  N0              4              139
  N1              3               50
  N2              2               32
  N3              1               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"
D70V7, binary
                  cls
clus                 0   1
  POLR2B MUTATED    10   0
  POLR2B WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED     10    0
  POLR2B WILD-TYPE  246   17
   clus
vv  POLR2B MUTATED POLR2B WILD-TYPE
  0             10              246
  1              0               17
[1] 2 2
[1] FALSE
D70V8, binary
                  cls
clus                 0   1
  POLR2B MUTATED     1   4
  POLR2B WILD-TYPE 106  69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      1    4
  POLR2B WILD-TYPE  106   69
     clus
vv    POLR2B MUTATED POLR2B WILD-TYPE
  NO               1              106
  YES              4               69
[1] 2 2
[1] FALSE
D70V9, binary
                  cls
clus                 0   1
  POLR2B MUTATED     1   9
  POLR2B WILD-TYPE  36 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      1    9
  POLR2B WILD-TYPE   36  244
     clus
vv    POLR2B MUTATED POLR2B WILD-TYPE
  NO               1               36
  YES              9              244
[1] 2 2
[1] FALSE
D70V10, continuous
D70V11, binary
                  cls
clus                 0   1
  POLR2B MUTATED     0  10
  POLR2B WILD-TYPE 109 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      0   10
  POLR2B WILD-TYPE  109  171
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  FEMALE              0              109
  MALE               10              171
[1] 2 2
[1] FALSE
D70V12, binary
                  cls
clus                 0   1
  POLR2B MUTATED    10   0
  POLR2B WILD-TYPE 244  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED     10    0
  POLR2B WILD-TYPE  244   35
     clus
vv    POLR2B MUTATED POLR2B WILD-TYPE
  NO              10              244
  YES              0               35
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POLR2B MUTATED       0                         0    10
  POLR2B WILD-TYPE     5                         1   274
D70V13, multiclass
                           clus
vv                          POLR2B MUTATED POLR2B WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 10              274
[1] 3 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
  POLR2B MUTATED     0  10
  POLR2B WILD-TYPE   3 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POLR2B MUTATED      0   10
  POLR2B WILD-TYPE    3  273
                        clus
vv                       POLR2B MUTATED POLR2B WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              273
[1] 2 2
[1] FALSE

Clustering(71) Variable = CSN3 MUTATION ANALYSIS
D71V1, survival
                sevent
clus2              0   1
  CSN3 MUTATED     4   0
  CSN3 WILD-TYPE  93 103
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            196 
  CSN3 MUTATED CSN3 WILD-TYPE 
             0            103 
$`CSN3 MUTATED`
TCGA-D3-A5GN TCGA-EE-A2M6 TCGA-FR-A3YN TCGA-FS-A1ZT 
       45.70       103.13         4.50        35.28 

$`CSN3 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
      144.46        31.76        62.70        11.34        42.05       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76         0.20        71.31        81.99        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1YW 
       68.52        15.48        32.05        74.47       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  CSN3 MUTATED CSN3 WILD-TYPE 
           4.5            0.0 
  CSN3 MUTATED CSN3 WILD-TYPE 
        103.13         346.49 
  CSN3 MUTATED CSN3 WILD-TYPE 
        40.490         47.575 
[1] "4.5 - 103.1 (40.5)" "0.0 - 346.5 (47.6)"
[1] "hr="     "9100000"
D71V2, survival
                sevent
clus2              0   1
  CSN3 MUTATED     4   0
  CSN3 WILD-TYPE 120 160
  CSN3 MUTATED CSN3 WILD-TYPE 
             4            280 
  CSN3 MUTATED CSN3 WILD-TYPE 
             0            160 
$`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-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       26.89       125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
       42.77        81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21        12.95       149.03       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        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  CSN3 MUTATED CSN3 WILD-TYPE 
         53.16           0.20 
  CSN3 MUTATED CSN3 WILD-TYPE 
        135.75         369.93 
  CSN3 MUTATED CSN3 WILD-TYPE 
       111.125         53.720 
[1] "53.2 - 135.8 (111.1)" "0.2 - 369.9 (53.7)"  
[1] "hr="     "9200000"
D71V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CSN3 MUTATED          0       0       2        0        1        0         0
  CSN3 WILD-TYPE       10       6      23       10       24       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CSN3 MUTATED           0         0         1          0          0          0
  CSN3 WILD-TYPE        14        10        35         14         26         43
                vv
clus             STAGE IV
  CSN3 MUTATED          0
  CSN3 WILD-TYPE       16
D71V4, multiclass
            clus
vv           CSN3 MUTATED CSN3 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               2             23
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             0             14
  STAGE IIC             0             10
  STAGE III             1             35
  STAGE IIIA            0             14
  STAGE IIIB            0             26
  STAGE IIIC            0             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
  CSN3 MUTATED       2  2  0  0
  CSN3 WILD-TYPE    51 60 60 55
D71V5, multiclass
       clus
vv      CSN3 MUTATED CSN3 WILD-TYPE
  T0+T1            2             51
  T2               2             60
  T3               0             60
  T4               0             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CSN3 MUTATED     3   1   0   0
  CSN3 WILD-TYPE 140  52  34  35
D71V6, multiclass
    clus
vv   CSN3 MUTATED CSN3 WILD-TYPE
  N0            3            140
  N1            1             52
  N2            0             34
  N3            0             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"
D71V7, binary
                cls
clus               0   1
  CSN3 MUTATED     4   0
  CSN3 WILD-TYPE 252  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      4    0
  CSN3 WILD-TYPE  252   17
   clus
vv  CSN3 MUTATED CSN3 WILD-TYPE
  0            4            252
  1            0             17
[1] 2 2
[1] FALSE
D71V8, binary
                cls
clus               0   1
  CSN3 MUTATED     2   0
  CSN3 WILD-TYPE 105  73
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      2    0
  CSN3 WILD-TYPE  105   73
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  NO             2            105
  YES            0             73
[1] 2 2
[1] FALSE
D71V9, binary
                cls
clus               0   1
  CSN3 MUTATED     0   4
  CSN3 WILD-TYPE  37 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      0    4
  CSN3 WILD-TYPE   37  249
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  NO             0             37
  YES            4            249
[1] 2 2
[1] FALSE
D71V10, continuous
D71V11, binary
                cls
clus               0   1
  CSN3 MUTATED     1   3
  CSN3 WILD-TYPE 108 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      1    3
  CSN3 WILD-TYPE  108  178
        clus
vv       CSN3 MUTATED CSN3 WILD-TYPE
  FEMALE            1            108
  MALE              3            178
[1] 2 2
[1] FALSE
D71V12, binary
                cls
clus               0   1
  CSN3 MUTATED     3   1
  CSN3 WILD-TYPE 251  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      3    1
  CSN3 WILD-TYPE  251   34
     clus
vv    CSN3 MUTATED CSN3 WILD-TYPE
  NO             3            251
  YES            1             34
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSN3 MUTATED       0                         0     4
  CSN3 WILD-TYPE     5                         1   280
D71V13, multiclass
                           clus
vv                          CSN3 MUTATED CSN3 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                4            280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                cls
clus               0   1
  CSN3 MUTATED     0   4
  CSN3 WILD-TYPE   3 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSN3 MUTATED      0    4
  CSN3 WILD-TYPE    3  279
                        clus
vv                       CSN3 MUTATED CSN3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            279
[1] 2 2
[1] FALSE

Clustering(72) Variable = CASP8 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     3   2
  CASP8 WILD-TYPE  94 101
  CASP8 MUTATED CASP8 WILD-TYPE 
              5             195 
  CASP8 MUTATED CASP8 WILD-TYPE 
              2             101 
$`CASP8 MUTATED`
TCGA-D3-A2JC TCGA-EE-A29M TCGA-EE-A2M6 TCGA-EE-A3JI TCGA-FS-A1Z3 
       86.30        47.74       103.13       135.98         8.35 

$`CASP8 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
        0.20        71.31        81.99        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 
      111.85        45.90         3.35       168.85        19.86        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
      195.98        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  CASP8 MUTATED CASP8 WILD-TYPE 
           8.35            0.00 
  CASP8 MUTATED CASP8 WILD-TYPE 
         135.98          346.49 
  CASP8 MUTATED CASP8 WILD-TYPE 
          86.30           46.92 
[1] "8.3 - 136.0 (86.3)" "0.0 - 346.5 (46.9)"
[1] "hr=" "1.4"
D72V2, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     3   3
  CASP8 WILD-TYPE 121 157
  CASP8 MUTATED CASP8 WILD-TYPE 
              6             278 
  CASP8 MUTATED CASP8 WILD-TYPE 
              3             157 
$`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        41.59       152.81        20.91 

$`CASP8 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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-A2JG TCGA-D3-A2JH 
       23.77       115.53       168.00        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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       13.97        63.78        72.07        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       81.21        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       180.39       216.66       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-A3AH 
      122.73        64.04        28.77        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-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      201.80        51.35       134.33        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         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        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  CASP8 MUTATED CASP8 WILD-TYPE 
          20.91            0.20 
  CASP8 MUTATED CASP8 WILD-TYPE 
         152.81          369.93 
  CASP8 MUTATED CASP8 WILD-TYPE 
          71.80           53.72 
[1] "20.9 - 152.8 (71.8)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1.2"
D72V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CASP8 MUTATED          2       0       2        0        1        0         0
  CASP8 WILD-TYPE        8       6      23       10       24       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CASP8 MUTATED           0         0         2          0          0
  CASP8 WILD-TYPE        14        10        34         14         26
                 vv
clus              STAGE IIIC STAGE IV
  CASP8 MUTATED            0        2
  CASP8 WILD-TYPE         43       14
D72V4, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  I/II NOS               2               8
  STAGE 0                0               6
  STAGE I                2              23
  STAGE IA               0              10
  STAGE IB               1              24
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              2              34
  STAGE IIIA             0              14
  STAGE IIIB             0              26
  STAGE IIIC             0              43
  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    50 59 60 55
D72V5, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1             3              50
  T2                3              59
  T3                0              60
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CASP8 MUTATED     6   0   2   0
  CASP8 WILD-TYPE 137  53  32  35
D72V6, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             6             137
  N1             0              53
  N2             2              32
  N3             0              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"
D72V7, binary
                 cls
clus                0   1
  CASP8 MUTATED     7   2
  CASP8 WILD-TYPE 249  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      7    2
  CASP8 WILD-TYPE  249   15
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0             7             249
  1             2              15
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus                0   1
  CASP8 MUTATED     3   0
  CASP8 WILD-TYPE 104  73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3    0
  CASP8 WILD-TYPE  104   73
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              3             104
  YES             0              73
[1] 2 2
[1] FALSE
D72V9, binary
                 cls
clus                0   1
  CASP8 MUTATED     3   6
  CASP8 WILD-TYPE  34 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      3    6
  CASP8 WILD-TYPE   34  247
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              3              34
  YES             6             247
[1] 2 2
[1] FALSE
D72V10, continuous
D72V11, binary
                 cls
clus                0   1
  CASP8 MUTATED     5   4
  CASP8 WILD-TYPE 104 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      5    4
  CASP8 WILD-TYPE  104  177
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             5             104
  MALE               4             177
[1] 2 2
[1] FALSE
D72V12, binary
                 cls
clus                0   1
  CASP8 MUTATED     8   1
  CASP8 WILD-TYPE 246  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      8    1
  CASP8 WILD-TYPE  246   34
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO              8             246
  YES             1              34
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED       0                         0     9
  CASP8 WILD-TYPE     5                         1   275
D72V13, multiclass
                           clus
vv                          CASP8 MUTATED CASP8 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 9             275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                 cls
clus                0   1
  CASP8 MUTATED     0   9
  CASP8 WILD-TYPE   3 274
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0    9
  CASP8 WILD-TYPE    3  274
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             9             274
[1] 2 2
[1] FALSE

Clustering(73) Variable = PPFIA1 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2               0  1
  PPFIA1 MUTATED    8  6
  PPFIA1 WILD-TYPE 89 97
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
              14              186 
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
               6               97 
$`PPFIA1 MUTATED`
TCGA-EE-A2GO TCGA-FW-A3R5 TCGA-D3-A51T TCGA-D3-A5GN TCGA-D9-A3Z3 TCGA-D9-A6EC 
       52.90        36.85        11.34        45.70        22.29        69.21 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A2MJ TCGA-EE-A3JI TCGA-FS-A1ZW 
       20.38        75.55        75.22        63.25       135.98        23.21 
TCGA-OD-A75X TCGA-RP-A693 
      297.01         0.33 

$`PPFIA1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
      134.40        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HV 
       62.70        42.05       177.86        15.02        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        24.89         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35       168.85        19.86        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A690 
        7.59       120.53        34.49        46.92         7.23         0.20 

  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
            0.33             0.00 
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
          297.01           346.49 
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
          49.300           47.295 
[1] "0.3 - 297.0 (49.3)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.2"
D73V2, survival
                  sevent
clus2                0   1
  PPFIA1 MUTATED     8   8
  PPFIA1 WILD-TYPE 116 152
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
              16              268 
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
               8              152 
$`PPFIA1 MUTATED`
TCGA-EE-A2GO TCGA-FW-A3R5 TCGA-D3-A51T TCGA-D3-A5GN TCGA-D9-A3Z3 TCGA-D9-A6EC 
      126.81        36.95        26.89       135.75        22.29        77.56 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A2MJ TCGA-EE-A3JI TCGA-FS-A1ZK 
       33.73       151.27        85.08        96.23       152.81        23.93 
TCGA-FS-A1ZW TCGA-GN-A266 TCGA-OD-A75X TCGA-RP-A693 
       49.48        10.13       297.90         0.33 

$`PPFIA1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL TCGA-D3-A5GO 
      145.12        32.94        22.62        63.81       125.79       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-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        7.10        15.39         9.90        25.18        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        14.70        26.89         4.96       133.81 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       91.56        13.55        63.35        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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 
       64.04        28.77        54.51        13.81        41.59       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-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      201.80        51.35       134.33        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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-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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.78       139.89       117.93        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A694 
       22.13         7.23         0.20         0.69 

  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
            0.33             0.20 
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
          297.90           369.93 
  PPFIA1 MUTATED PPFIA1 WILD-TYPE 
           63.52            53.97 
[1] "0.3 - 297.9 (63.5)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.2"
D73V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PPFIA1 MUTATED          0       1       2        0        0        3
  PPFIA1 WILD-TYPE       10       5      23       10       25       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PPFIA1 MUTATED           0         1         0         2          1
  PPFIA1 WILD-TYPE        10        13        10        34         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PPFIA1 MUTATED            2          1        1
  PPFIA1 WILD-TYPE         24         42       15
D73V4, multiclass
            clus
vv           PPFIA1 MUTATED PPFIA1 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 1                5
  STAGE I                 2               23
  STAGE IA                0               10
  STAGE IB                0               25
  STAGE II                3               15
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               2               34
  STAGE IIIA              1               13
  STAGE IIIB              2               24
  STAGE IIIC              1               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
  PPFIA1 MUTATED       1  2  5  3
  PPFIA1 WILD-TYPE    52 60 55 52
D73V5, multiclass
       clus
vv      PPFIA1 MUTATED PPFIA1 WILD-TYPE
  T0+T1              1               52
  T2                 2               60
  T3                 5               55
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PPFIA1 MUTATED     8   4   1   0
  PPFIA1 WILD-TYPE 135  49  33  35
D73V6, multiclass
    clus
vv   PPFIA1 MUTATED PPFIA1 WILD-TYPE
  N0              8              135
  N1              4               49
  N2              1               33
  N3              0               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"
D73V7, binary
                  cls
clus                 0   1
  PPFIA1 MUTATED    14   1
  PPFIA1 WILD-TYPE 242  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA1 MUTATED     14    1
  PPFIA1 WILD-TYPE  242   16
   clus
vv  PPFIA1 MUTATED PPFIA1 WILD-TYPE
  0             14              242
  1              1               16
[1] 2 2
[1] FALSE
D73V8, binary
                  cls
clus                 0   1
  PPFIA1 MUTATED     5   3
  PPFIA1 WILD-TYPE 102  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA1 MUTATED      5    3
  PPFIA1 WILD-TYPE  102   70
     clus
vv    PPFIA1 MUTATED PPFIA1 WILD-TYPE
  NO               5              102
  YES              3               70
[1] 2 2
[1] FALSE
D73V9, binary
                  cls
clus                 0   1
  PPFIA1 MUTATED     2  14
  PPFIA1 WILD-TYPE  35 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA1 MUTATED      2   14
  PPFIA1 WILD-TYPE   35  239
     clus
vv    PPFIA1 MUTATED PPFIA1 WILD-TYPE
  NO               2               35
  YES             14              239
[1] 2 2
[1] FALSE
D73V10, continuous
D73V11, binary
                  cls
clus                 0   1
  PPFIA1 MUTATED     5  11
  PPFIA1 WILD-TYPE 104 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA1 MUTATED      5   11
  PPFIA1 WILD-TYPE  104  170
        clus
vv       PPFIA1 MUTATED PPFIA1 WILD-TYPE
  FEMALE              5              104
  MALE               11              170
[1] 2 2
[1] FALSE
D73V12, binary
                  cls
clus                 0   1
  PPFIA1 MUTATED    12   4
  PPFIA1 WILD-TYPE 242  31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA1 MUTATED     12    4
  PPFIA1 WILD-TYPE  242   31
     clus
vv    PPFIA1 MUTATED PPFIA1 WILD-TYPE
  NO              12              242
  YES              4               31
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPFIA1 MUTATED       0                         0    16
  PPFIA1 WILD-TYPE     5                         1   268
D73V13, multiclass
                           clus
vv                          PPFIA1 MUTATED PPFIA1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 16              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
  PPFIA1 MUTATED     0  16
  PPFIA1 WILD-TYPE   3 267
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA1 MUTATED      0   16
  PPFIA1 WILD-TYPE    3  267
                        clus
vv                       PPFIA1 MUTATED PPFIA1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             16              267
[1] 2 2
[1] FALSE

Clustering(74) Variable = ZNF490 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2               0  1
  ZNF490 MUTATED    5  5
  ZNF490 WILD-TYPE 92 98
  ZNF490 MUTATED ZNF490 WILD-TYPE 
              10              190 
  ZNF490 MUTATED ZNF490 WILD-TYPE 
               5               98 
$`ZNF490 MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A3JI TCGA-ER-A19A 
      134.40        36.85        24.89         0.00       135.98         4.54 
TCGA-ER-A19W TCGA-FR-A3YN TCGA-FS-A1ZZ TCGA-QB-A6FS 
      146.63         4.50         3.06         7.23 

$`ZNF490 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       13.15        20.38        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35       168.85        19.86        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        7.82        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A 
      173.29        68.52        15.48        32.05        74.47       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      136.27        35.28         4.47        23.21         5.29        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         0.20         0.33 

  ZNF490 MUTATED ZNF490 WILD-TYPE 
             0.0              0.2 
  ZNF490 MUTATED ZNF490 WILD-TYPE 
          146.63           346.49 
  ZNF490 MUTATED ZNF490 WILD-TYPE 
          16.060           48.545 
[1] "0.0 - 146.6 (16.1)" "0.2 - 346.5 (48.5)"
[1] "hr=" "1.5"
D74V2, survival
                  sevent
clus2                0   1
  ZNF490 MUTATED     6  10
  ZNF490 WILD-TYPE 118 150
  ZNF490 MUTATED ZNF490 WILD-TYPE 
              16              268 
  ZNF490 MUTATED ZNF490 WILD-TYPE 
              10              150 
$`ZNF490 MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A5GO TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-EE-A17Y 
      134.40        36.95       137.92         7.10        20.38        27.22 
TCGA-EE-A182 TCGA-EE-A29V TCGA-EE-A3JI TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19W 
       14.70        25.87       152.81        77.75        13.02       148.18 
TCGA-FR-A3YN TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-QB-A6FS 
       92.98        27.02        28.73         7.23 

$`ZNF490 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       126.81        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        3.65        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        76.57        36.03       144.89       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       29.82         8.65        33.73        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29W 
       56.42        66.74        14.47        61.28       369.93       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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-A195 
       34.32        53.19       201.80        51.35       134.33        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       13.94         9.17        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        49.48         8.88       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A 
       93.01        46.98        33.21        12.95       149.03       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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       49.48        27.09        77.82        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         0.20         0.33         0.69 

  ZNF490 MUTATED ZNF490 WILD-TYPE 
             7.1              0.2 
  ZNF490 MUTATED ZNF490 WILD-TYPE 
          152.81           369.93 
  ZNF490 MUTATED ZNF490 WILD-TYPE 
          27.975           54.460 
[1] "7.1 - 152.8 (28.0)" "0.2 - 369.9 (54.5)"
[1] "hr=" "1.5"
D74V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ZNF490 MUTATED          0       0       2        0        3        1
  ZNF490 WILD-TYPE       10       6      23       10       22       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ZNF490 MUTATED           0         1         0         1          0
  ZNF490 WILD-TYPE        10        13        10        35         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ZNF490 MUTATED            1          3        2
  ZNF490 WILD-TYPE         25         40       14
D74V4, multiclass
            clus
vv           ZNF490 MUTATED ZNF490 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 2               23
  STAGE IA                0               10
  STAGE IB                3               22
  STAGE II                1               17
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               1               35
  STAGE IIIA              0               14
  STAGE IIIB              1               25
  STAGE IIIC              3               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
  ZNF490 MUTATED       1  5  3  3
  ZNF490 WILD-TYPE    52 57 57 52
D74V5, multiclass
       clus
vv      ZNF490 MUTATED ZNF490 WILD-TYPE
  T0+T1              1               52
  T2                 5               57
  T3                 3               57
  T4                 3               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF490 MUTATED     8   3   1   2
  ZNF490 WILD-TYPE 135  50  33  33
D74V6, multiclass
    clus
vv   ZNF490 MUTATED ZNF490 WILD-TYPE
  N0              8              135
  N1              3               50
  N2              1               33
  N3              2               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"
D74V7, binary
                  cls
clus                 0   1
  ZNF490 MUTATED    13   2
  ZNF490 WILD-TYPE 243  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF490 MUTATED     13    2
  ZNF490 WILD-TYPE  243   15
   clus
vv  ZNF490 MUTATED ZNF490 WILD-TYPE
  0             13              243
  1              2               15
[1] 2 2
[1] FALSE
D74V8, binary
                  cls
clus                 0   1
  ZNF490 MUTATED     7   5
  ZNF490 WILD-TYPE 100  68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF490 MUTATED      7    5
  ZNF490 WILD-TYPE  100   68
     clus
vv    ZNF490 MUTATED ZNF490 WILD-TYPE
  NO               7              100
  YES              5               68
[1] 2 2
[1] FALSE
D74V9, binary
                  cls
clus                 0   1
  ZNF490 MUTATED     2  14
  ZNF490 WILD-TYPE  35 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF490 MUTATED      2   14
  ZNF490 WILD-TYPE   35  239
     clus
vv    ZNF490 MUTATED ZNF490 WILD-TYPE
  NO               2               35
  YES             14              239
[1] 2 2
[1] FALSE
D74V10, continuous
D74V11, binary
                  cls
clus                 0   1
  ZNF490 MUTATED     6  10
  ZNF490 WILD-TYPE 103 171
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF490 MUTATED      6   10
  ZNF490 WILD-TYPE  103  171
        clus
vv       ZNF490 MUTATED ZNF490 WILD-TYPE
  FEMALE              6              103
  MALE               10              171
[1] 2 2
[1] FALSE
D74V12, binary
                  cls
clus                 0   1
  ZNF490 MUTATED    13   3
  ZNF490 WILD-TYPE 241  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF490 MUTATED     13    3
  ZNF490 WILD-TYPE  241   32
     clus
vv    ZNF490 MUTATED ZNF490 WILD-TYPE
  NO              13              241
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF490 MUTATED       1                         0    15
  ZNF490 WILD-TYPE     4                         1   269
D74V13, multiclass
                           clus
vv                          ZNF490 MUTATED ZNF490 WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 15              269
[1] 3 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
  ZNF490 MUTATED     1  14
  ZNF490 WILD-TYPE   2 269
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF490 MUTATED      1   14
  ZNF490 WILD-TYPE    2  269
                        clus
vv                       ZNF490 MUTATED ZNF490 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             14              269
[1] 2 2
[1] FALSE

Clustering(75) Variable = IL5RA MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2              0  1
  IL5RA MUTATED    5  7
  IL5RA WILD-TYPE 92 96
  IL5RA MUTATED IL5RA WILD-TYPE 
             12             188 
  IL5RA MUTATED IL5RA WILD-TYPE 
              7              96 
$`IL5RA MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A51T TCGA-EE-A17X 
      134.40        27.35        19.04        36.85        11.34        13.15 
TCGA-EE-A17Y TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-ER-A19C TCGA-FS-A4FD 
       24.89        63.25       143.93        54.51        39.81        80.68 

$`IL5RA WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       52.90         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
      173.85        30.67       144.46        31.76        62.70        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       45.70       177.86        15.02        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       16.41        52.41        18.21        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK 
        5.75        23.77       209.79        94.19       171.85        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      104.78       145.45       227.01        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        64.04         4.41         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       10.49         7.82         4.54        53.29        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       13.28        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  IL5RA MUTATED IL5RA WILD-TYPE 
          11.34            0.00 
  IL5RA MUTATED IL5RA WILD-TYPE 
         143.93          346.49 
  IL5RA MUTATED IL5RA WILD-TYPE 
         38.330          47.575 
[1] "11.3 - 143.9 (38.3)" "0.0 - 346.5 (47.6)" 
[1] "hr=" "1.5"
D75V2, survival
                 sevent
clus2               0   1
  IL5RA MUTATED     5  11
  IL5RA WILD-TYPE 119 149
  IL5RA MUTATED IL5RA WILD-TYPE 
             16             268 
  IL5RA MUTATED IL5RA WILD-TYPE 
             11             149 
$`IL5RA MUTATED`
TCGA-EE-A29L TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A51T 
        2.60       134.40        27.35        31.40        36.95        26.89 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3J5 
       29.82        27.22        96.23       162.48        54.51        36.95 
TCGA-ER-A19C TCGA-FS-A4FC TCGA-FS-A4FD TCGA-GN-A266 
       48.89        54.41        80.68        10.13 

$`IL5RA WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A198 TCGA-FS-A1ZF 
       68.15       168.26       340.14       126.81        50.76        15.45 
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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       20.35        29.29        58.92         7.04        36.46         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       180.39       216.66       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-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       64.04        28.77        13.81        41.59       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-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
      174.84        34.03        26.73        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  IL5RA MUTATED IL5RA WILD-TYPE 
            2.6             0.2 
  IL5RA MUTATED IL5RA WILD-TYPE 
         162.48          369.93 
  IL5RA MUTATED IL5RA WILD-TYPE 
         36.950          54.705 
[1] "2.6 - 162.5 (37.0)" "0.2 - 369.9 (54.7)"
[1] "hr=" "1.7"
D75V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  IL5RA MUTATED          0       0       2        2        0        1         1
  IL5RA WILD-TYPE       10       6      23        8       25       17         9
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  IL5RA MUTATED           1         0         4          0          1
  IL5RA WILD-TYPE        13        10        32         14         25
                 vv
clus              STAGE IIIC STAGE IV
  IL5RA MUTATED            3        0
  IL5RA WILD-TYPE         40       16
D75V4, multiclass
            clus
vv           IL5RA MUTATED IL5RA WILD-TYPE
  I/II NOS               0              10
  STAGE 0                0               6
  STAGE I                2              23
  STAGE IA               2               8
  STAGE IB               0              25
  STAGE II               1              17
  STAGE IIA              1               9
  STAGE IIB              1              13
  STAGE IIC              0              10
  STAGE III              4              32
  STAGE IIIA             0              14
  STAGE IIIB             1              25
  STAGE IIIC             3              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
  IL5RA MUTATED       2  3  4  4
  IL5RA WILD-TYPE    51 59 56 51
D75V5, multiclass
       clus
vv      IL5RA MUTATED IL5RA WILD-TYPE
  T0+T1             2              51
  T2                3              59
  T3                4              56
  T4                4              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IL5RA MUTATED     7   3   2   2
  IL5RA WILD-TYPE 136  50  32  33
D75V6, multiclass
    clus
vv   IL5RA MUTATED IL5RA WILD-TYPE
  N0             7             136
  N1             3              50
  N2             2              32
  N3             2              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"
D75V7, binary
                 cls
clus                0   1
  IL5RA MUTATED    15   0
  IL5RA WILD-TYPE 241  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED     15    0
  IL5RA WILD-TYPE  241   17
   clus
vv  IL5RA MUTATED IL5RA WILD-TYPE
  0            15             241
  1             0              17
[1] 2 2
[1] FALSE
D75V8, binary
                 cls
clus               0  1
  IL5RA MUTATED    9  3
  IL5RA WILD-TYPE 98 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      9    3
  IL5RA WILD-TYPE   98   70
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  NO              9              98
  YES             3              70
[1] 2 2
[1] FALSE
D75V9, binary
                 cls
clus                0   1
  IL5RA MUTATED     2  14
  IL5RA WILD-TYPE  35 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      2   14
  IL5RA WILD-TYPE   35  239
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  NO              2              35
  YES            14             239
[1] 2 2
[1] FALSE
D75V10, continuous
D75V11, binary
                 cls
clus                0   1
  IL5RA MUTATED     3  13
  IL5RA WILD-TYPE 106 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      3   13
  IL5RA WILD-TYPE  106  168
        clus
vv       IL5RA MUTATED IL5RA WILD-TYPE
  FEMALE             3             106
  MALE              13             168
[1] 2 2
[1] FALSE
D75V12, binary
                 cls
clus                0   1
  IL5RA MUTATED    13   3
  IL5RA WILD-TYPE 241  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED     13    3
  IL5RA WILD-TYPE  241   32
     clus
vv    IL5RA MUTATED IL5RA WILD-TYPE
  NO             13             241
  YES             3              32
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL5RA MUTATED       1                         0    15
  IL5RA WILD-TYPE     4                         1   269
D75V13, multiclass
                           clus
vv                          IL5RA MUTATED IL5RA WILD-TYPE
  ASIAN                                 1               4
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                15             269
[1] 3 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
  IL5RA MUTATED     0  14
  IL5RA WILD-TYPE   3 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL5RA MUTATED      0   14
  IL5RA WILD-TYPE    3  269
                        clus
vv                       IL5RA MUTATED IL5RA WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            14             269
[1] 2 2
[1] FALSE

Clustering(76) Variable = LILRB5 MUTATION ANALYSIS
D76V1, survival
                  sevent
clus2               0  1
  LILRB5 MUTATED    9  4
  LILRB5 WILD-TYPE 88 99
  LILRB5 MUTATED LILRB5 WILD-TYPE 
              13              187 
  LILRB5 MUTATED LILRB5 WILD-TYPE 
               4               99 
$`LILRB5 MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A51R 
      134.40        27.35        36.85        45.99        62.86        62.70 
TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-EE-A2A2 TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AA 
       76.34        60.10        30.02        89.26       143.93       124.31 
TCGA-FS-A1ZZ 
        3.06 

$`LILRB5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.90        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       144.46        31.76        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
      177.86        15.02        22.29        69.21        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       68.68       150.61       110.53        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        63.25       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      227.01        23.51        53.26       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        5.29        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  LILRB5 MUTATED LILRB5 WILD-TYPE 
            3.06             0.00 
  LILRB5 MUTATED LILRB5 WILD-TYPE 
          143.93           346.49 
  LILRB5 MUTATED LILRB5 WILD-TYPE 
           62.70            46.92 
[1] "3.1 - 143.9 (62.7)" "0.0 - 346.5 (46.9)"
[1] "hr=" "1.7"
D76V2, survival
                  sevent
clus2                0   1
  LILRB5 MUTATED    12   7
  LILRB5 WILD-TYPE 112 153
  LILRB5 MUTATED LILRB5 WILD-TYPE 
              19              265 
  LILRB5 MUTATED LILRB5 WILD-TYPE 
               7              153 
$`LILRB5 MUTATED`
TCGA-D3-A3ML TCGA-EE-A29L TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2J7 
       13.87         2.60       134.40        27.35        36.95       103.10 
TCGA-D3-A2J8 TCGA-D3-A51R TCGA-D3-A5GU TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-EE-A2A2 
       65.49        63.81       125.19        76.57        88.87        59.64 
TCGA-EE-A2GI TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-FS-A1ZZ 
       48.72       180.39       162.48       124.31        36.95        27.02 
TCGA-GF-A6C9 
       15.78 

$`LILRB5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      168.26       340.14       126.81        31.40        50.76        15.45 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        22.62        26.89       125.79 
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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       77.56        22.95        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93       135.02        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
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-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
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       173.79       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66        96.23       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       47.54       248.65        43.23        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  LILRB5 MUTATED LILRB5 WILD-TYPE 
             2.6              0.2 
  LILRB5 MUTATED LILRB5 WILD-TYPE 
          180.39           369.93 
  LILRB5 MUTATED LILRB5 WILD-TYPE 
           63.81            53.52 
[1] "2.6 - 180.4 (63.8)" "0.2 - 369.9 (53.5)"
[1] "hr=" "1.5"
D76V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  LILRB5 MUTATED          0       0       1        1        2        1
  LILRB5 WILD-TYPE       10       6      24        9       23       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  LILRB5 MUTATED           1         1         0         5          1
  LILRB5 WILD-TYPE         9        13        10        31         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  LILRB5 MUTATED            3          3        0
  LILRB5 WILD-TYPE         23         40       16
D76V4, multiclass
            clus
vv           LILRB5 MUTATED LILRB5 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                1                9
  STAGE IB                2               23
  STAGE II                1               17
  STAGE IIA               1                9
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               5               31
  STAGE IIIA              1               13
  STAGE IIIB              3               23
  STAGE IIIC              3               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
  LILRB5 MUTATED       5  2  5  4
  LILRB5 WILD-TYPE    48 60 55 51
D76V5, multiclass
       clus
vv      LILRB5 MUTATED LILRB5 WILD-TYPE
  T0+T1              5               48
  T2                 2               60
  T3                 5               55
  T4                 4               51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  LILRB5 MUTATED     8   3   6   1
  LILRB5 WILD-TYPE 135  50  28  34
D76V6, multiclass
    clus
vv   LILRB5 MUTATED LILRB5 WILD-TYPE
  N0              8              135
  N1              3               50
  N2              6               28
  N3              1               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"
D76V7, binary
                  cls
clus                 0   1
  LILRB5 MUTATED    18   0
  LILRB5 WILD-TYPE 238  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB5 MUTATED     18    0
  LILRB5 WILD-TYPE  238   17
   clus
vv  LILRB5 MUTATED LILRB5 WILD-TYPE
  0             18              238
  1              0               17
[1] 2 2
[1] FALSE
D76V8, binary
                  cls
clus                0  1
  LILRB5 MUTATED    9  4
  LILRB5 WILD-TYPE 98 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB5 MUTATED      9    4
  LILRB5 WILD-TYPE   98   69
     clus
vv    LILRB5 MUTATED LILRB5 WILD-TYPE
  NO               9               98
  YES              4               69
[1] 2 2
[1] FALSE
D76V9, binary
                  cls
clus                 0   1
  LILRB5 MUTATED     5  14
  LILRB5 WILD-TYPE  32 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB5 MUTATED      5   14
  LILRB5 WILD-TYPE   32  239
     clus
vv    LILRB5 MUTATED LILRB5 WILD-TYPE
  NO               5               32
  YES             14              239
[1] 2 2
[1] FALSE
D76V10, continuous
D76V11, binary
                  cls
clus                 0   1
  LILRB5 MUTATED     3  16
  LILRB5 WILD-TYPE 106 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB5 MUTATED      3   16
  LILRB5 WILD-TYPE  106  165
        clus
vv       LILRB5 MUTATED LILRB5 WILD-TYPE
  FEMALE              3              106
  MALE               16              165
[1] 2 2
[1] FALSE
D76V12, binary
                  cls
clus                 0   1
  LILRB5 MUTATED    16   3
  LILRB5 WILD-TYPE 238  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB5 MUTATED     16    3
  LILRB5 WILD-TYPE  238   32
     clus
vv    LILRB5 MUTATED LILRB5 WILD-TYPE
  NO              16              238
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LILRB5 MUTATED       0                         0    19
  LILRB5 WILD-TYPE     5                         1   265
D76V13, multiclass
                           clus
vv                          LILRB5 MUTATED LILRB5 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 19              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"
D76V14, binary
                  cls
clus                 0   1
  LILRB5 MUTATED     1  18
  LILRB5 WILD-TYPE   2 265
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB5 MUTATED      1   18
  LILRB5 WILD-TYPE    2  265
                        clus
vv                       LILRB5 MUTATED LILRB5 WILD-TYPE
  HISPANIC OR LATINO                  1                2
  NOT HISPANIC OR LATINO             18              265
[1] 2 2
[1] FALSE

Clustering(77) Variable = C10ORF72 MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  C10ORF72 MUTATED    8  5
  C10ORF72 WILD-TYPE 89 98
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
                13                187 
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
                 5                 98 
$`C10ORF72 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-D9-A6EC 
       38.76       134.40        27.35        36.85        62.86        69.21 
TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GB TCGA-EE-A3AA TCGA-EE-A3AC 
       75.55        12.99         0.26        26.14       124.31        64.04 
TCGA-GN-A268 
       42.48 

$`C10ORF72 WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        33.24        31.96       166.75       269.03        52.90 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL 
       15.75       168.00        86.30       107.61        36.30       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.83        66.08        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       59.70        24.53         9.34        90.21        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV 
       45.70       177.86        15.02        22.29        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       26.24        79.20        75.22        76.14        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       30.02        77.98        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD 
      227.01       143.93        23.51        53.26       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        1.91        53.29       117.93        96.92        17.06         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
              0.26               0.00 
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
            134.40             346.49 
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
             42.48              47.41 
[1] "0.3 - 134.4 (42.5)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.1"
D77V2, survival
                    sevent
clus2                  0   1
  C10ORF72 MUTATED     9  10
  C10ORF72 WILD-TYPE 115 150
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
                19                265 
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
                10                150 
$`C10ORF72 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-D9-A6EC 
       46.32       134.40        27.35        36.95        65.49        77.56 
TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GB TCGA-EE-A2M5 
      151.27        63.35        13.97        63.78        59.28        21.67 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-FS-A1ZB TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A266 
      124.31        64.04        48.85        28.73        15.78        10.13 
TCGA-GN-A268 
       62.79 

$`C10ORF72 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 TCGA-ER-A198 
      168.26         2.60       340.14       126.81        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       15.39        22.29         9.90        25.18        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
      133.81        91.56        13.55        85.08        78.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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 
      115.96        59.64        39.29        86.14        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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-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       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      216.66       167.90        47.54       248.65        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       71.21        53.26       122.73        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        27.72       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        19.43         2.04       139.89       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
             10.13               0.20 
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
            151.27             369.93 
  C10ORF72 MUTATED C10ORF72 WILD-TYPE 
             59.28              53.92 
[1] "10.1 - 151.3 (59.3)" "0.2 - 369.9 (53.9)" 
[1] "hr=" "1.2"
D77V3, continuous
                    vv
clus                 I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C10ORF72 MUTATED          0       1       2        0        2        1
  C10ORF72 WILD-TYPE       10       5      23       10       23       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C10ORF72 MUTATED           0         1         0         4          2
  C10ORF72 WILD-TYPE        10        13        10        32         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  C10ORF72 MUTATED            3          2        1
  C10ORF72 WILD-TYPE         23         41       15
D77V4, multiclass
            clus
vv           C10ORF72 MUTATED C10ORF72 WILD-TYPE
  I/II NOS                  0                 10
  STAGE 0                   1                  5
  STAGE I                   2                 23
  STAGE IA                  0                 10
  STAGE IB                  2                 23
  STAGE II                  1                 17
  STAGE IIA                 0                 10
  STAGE IIB                 1                 13
  STAGE IIC                 0                 10
  STAGE III                 4                 32
  STAGE IIIA                2                 12
  STAGE IIIB                3                 23
  STAGE IIIC                2                 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
  C10ORF72 MUTATED       2  5  5  1
  C10ORF72 WILD-TYPE    51 57 55 54
D77V5, multiclass
       clus
vv      C10ORF72 MUTATED C10ORF72 WILD-TYPE
  T0+T1                2                 51
  T2                   5                 57
  T3                   5                 55
  T4                   1                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C10ORF72 MUTATED     7   5   4   1
  C10ORF72 WILD-TYPE 136  48  30  34
D77V6, multiclass
    clus
vv   C10ORF72 MUTATED C10ORF72 WILD-TYPE
  N0                7                136
  N1                5                 48
  N2                4                 30
  N3                1                 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"
D77V7, binary
                    cls
clus                   0   1
  C10ORF72 MUTATED    17   1
  C10ORF72 WILD-TYPE 239  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF72 MUTATED     17    1
  C10ORF72 WILD-TYPE  239   16
   clus
vv  C10ORF72 MUTATED C10ORF72 WILD-TYPE
  0               17                239
  1                1                 16
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                  0  1
  C10ORF72 MUTATED    9  2
  C10ORF72 WILD-TYPE 98 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF72 MUTATED      9    2
  C10ORF72 WILD-TYPE   98   71
     clus
vv    C10ORF72 MUTATED C10ORF72 WILD-TYPE
  NO                 9                 98
  YES                2                 71
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                   0   1
  C10ORF72 MUTATED     5  15
  C10ORF72 WILD-TYPE  32 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF72 MUTATED      5   15
  C10ORF72 WILD-TYPE   32  238
     clus
vv    C10ORF72 MUTATED C10ORF72 WILD-TYPE
  NO                 5                 32
  YES               15                238
[1] 2 2
[1] FALSE
D77V10, continuous
D77V11, binary
                    cls
clus                   0   1
  C10ORF72 MUTATED     3  17
  C10ORF72 WILD-TYPE 106 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF72 MUTATED      3   17
  C10ORF72 WILD-TYPE  106  164
        clus
vv       C10ORF72 MUTATED C10ORF72 WILD-TYPE
  FEMALE                3                106
  MALE                 17                164
[1] 2 2
[1] FALSE
D77V12, binary
                    cls
clus                   0   1
  C10ORF72 MUTATED    15   5
  C10ORF72 WILD-TYPE 239  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF72 MUTATED     15    5
  C10ORF72 WILD-TYPE  239   30
     clus
vv    C10ORF72 MUTATED C10ORF72 WILD-TYPE
  NO                15                239
  YES                5                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C10ORF72 MUTATED       0                         0    20
  C10ORF72 WILD-TYPE     5                         1   264
D77V13, multiclass
                           clus
vv                          C10ORF72 MUTATED C10ORF72 WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   20                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"
D77V14, binary
                    cls
clus                   0   1
  C10ORF72 MUTATED     0  19
  C10ORF72 WILD-TYPE   3 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF72 MUTATED      0   19
  C10ORF72 WILD-TYPE    3  264
                        clus
vv                       C10ORF72 MUTATED C10ORF72 WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               19                264
[1] 2 2
[1] FALSE

Clustering(78) Variable = C3ORF71 MUTATION ANALYSIS
D78V1, survival
                   sevent
clus2                 0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE  96 100
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               196 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                3               100 
$`C3ORF71 MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A2GL TCGA-EE-A2MC TCGA-ER-A2NC 
      110.93        32.48        23.77        22.36 

$`C3ORF71 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       15.72        31.89        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      201.60        68.65        10.62        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      120.76        49.71        47.18       146.63        73.05         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
            22.36              0.00 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
           110.93            346.49 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
           28.125            47.575 
[1] "22.4 - 110.9 (28.1)" "0.0 - 346.5 (47.6)" 
[1] "hr=" "2.1"
D78V2, survival
                   sevent
clus2                 0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 123 157
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                4               280 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
                3               157 
$`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-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
      107.38        54.74        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18       105.07        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
            43.82              0.20 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
           112.57            369.93 
  C3ORF71 MUTATED C3ORF71 WILD-TYPE 
           70.585            53.720 
[1] "43.8 - 112.6 (70.6)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1.3"
D78V3, continuous
                   vv
clus                I/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      24       10       24       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C3ORF71 MUTATED           1         0         0         0          0
  C3ORF71 WILD-TYPE         9        14        10        36         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C3ORF71 MUTATED            0          0        0
  C3ORF71 WILD-TYPE         26         43       16
D78V4, multiclass
            clus
vv           C3ORF71 MUTATED C3ORF71 WILD-TYPE
  I/II NOS                 1                 9
  STAGE 0                  0                 6
  STAGE I                  1                24
  STAGE IA                 0                10
  STAGE IB                 1                24
  STAGE II                 0                18
  STAGE IIA                1                 9
  STAGE IIB                0                14
  STAGE IIC                0                10
  STAGE III                0                36
  STAGE IIIA               0                14
  STAGE IIIB               0                26
  STAGE IIIC               0                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
  C3ORF71 MUTATED       0  2  1  0
  C3ORF71 WILD-TYPE    53 60 59 55
D78V5, multiclass
       clus
vv      C3ORF71 MUTATED C3ORF71 WILD-TYPE
  T0+T1               0                53
  T2                  2                60
  T3                  1                59
  T4                  0                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C3ORF71 MUTATED     4   0   0   0
  C3ORF71 WILD-TYPE 139  53  34  35
D78V6, multiclass
    clus
vv   C3ORF71 MUTATED C3ORF71 WILD-TYPE
  N0               4               139
  N1               0                53
  N2               0                34
  N3               0                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"
D78V7, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     4   0
  C3ORF71 WILD-TYPE 252  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      4    0
  C3ORF71 WILD-TYPE  252   17
   clus
vv  C3ORF71 MUTATED C3ORF71 WILD-TYPE
  0               4               252
  1               0                17
[1] 2 2
[1] FALSE
D78V8, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     3   0
  C3ORF71 WILD-TYPE 104  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      3    0
  C3ORF71 WILD-TYPE  104   73
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  NO                3               104
  YES               0                73
[1] 2 2
[1] FALSE
D78V9, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     0   4
  C3ORF71 WILD-TYPE  37 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      0    4
  C3ORF71 WILD-TYPE   37  249
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  NO                0                37
  YES               4               249
[1] 2 2
[1] FALSE
D78V10, continuous
D78V11, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     1   3
  C3ORF71 WILD-TYPE 108 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      1    3
  C3ORF71 WILD-TYPE  108  178
        clus
vv       C3ORF71 MUTATED C3ORF71 WILD-TYPE
  FEMALE               1               108
  MALE                 3               178
[1] 2 2
[1] FALSE
D78V12, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     4   0
  C3ORF71 WILD-TYPE 250  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      4    0
  C3ORF71 WILD-TYPE  250   35
     clus
vv    C3ORF71 MUTATED C3ORF71 WILD-TYPE
  NO                4               250
  YES               0                35
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3ORF71 MUTATED       0                         0     4
  C3ORF71 WILD-TYPE     5                         1   280
D78V13, multiclass
                           clus
vv                          C3ORF71 MUTATED C3ORF71 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4               280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                   cls
clus                  0   1
  C3ORF71 MUTATED     0   4
  C3ORF71 WILD-TYPE   3 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF71 MUTATED      0    4
  C3ORF71 WILD-TYPE    3  279
                        clus
vv                       C3ORF71 MUTATED C3ORF71 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               279
[1] 2 2
[1] FALSE

Clustering(79) Variable = ZNF589 MUTATION ANALYSIS
D79V1, survival
                  sevent
clus2                0   1
  ZNF589 MUTATED     0   2
  ZNF589 WILD-TYPE  97 101
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               2              198 
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               2              101 
$`ZNF589 MUTATED`
TCGA-EE-A3JD TCGA-EE-A3JI 
       27.35       135.98 

$`ZNF589 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       75.55        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       19.86        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  ZNF589 MUTATED ZNF589 WILD-TYPE 
           27.35             0.00 
  ZNF589 MUTATED ZNF589 WILD-TYPE 
          135.98           346.49 
  ZNF589 MUTATED ZNF589 WILD-TYPE 
          81.665           47.295 
[1] "27.4 - 136.0 (81.7)" "0.0 - 346.5 (47.3)" 
[1] "Remove cluster labels:" "ZNF589 MUTATED"        
D79V2, survival
                  sevent
clus2                0   1
  ZNF589 MUTATED     1   2
  ZNF589 WILD-TYPE 123 158
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               3              281 
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               2              158 
$`ZNF589 MUTATED`
TCGA-EE-A3JD TCGA-D9-A1JW TCGA-EE-A3JI 
       27.35         3.65       152.81 

$`ZNF589 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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-A195 
       34.32        53.19       201.80        51.35       134.33        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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        46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  ZNF589 MUTATED ZNF589 WILD-TYPE 
            3.65             0.20 
  ZNF589 MUTATED ZNF589 WILD-TYPE 
          152.81           369.93 
  ZNF589 MUTATED ZNF589 WILD-TYPE 
           27.35            54.02 
[1] "3.6 - 152.8 (27.4)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.6"
D79V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ZNF589 MUTATED          0       0       1        0        0        0
  ZNF589 WILD-TYPE       10       6      24       10       25       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ZNF589 MUTATED           0         0         0         1          0
  ZNF589 WILD-TYPE        10        14        10        35         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ZNF589 MUTATED            0          0        0
  ZNF589 WILD-TYPE         26         43       16
D79V4, multiclass
[1] "Remove cluster labels:" "ZNF589 MUTATED"        
clus
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               2              261 
      TCGA-D3-A2JF       TCGA-D3-A3C8       TCGA-D3-A3ML       TCGA-D3-A51G 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EB-A5SH       TCGA-EE-A180       TCGA-EE-A184       TCGA-EE-A20H 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29L       TCGA-EE-A2GD       TCGA-EE-A2GO       TCGA-EE-A2MR 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A193       TCGA-FR-A3YO       TCGA-FS-A1ZF       TCGA-FW-A3R5 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q3       TCGA-D3-A1Q4       TCGA-D3-A1Q5 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A1Q6       TCGA-D3-A1Q7       TCGA-D3-A1Q8       TCGA-D3-A1Q9 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A1QA       TCGA-D3-A1QB       TCGA-D3-A2J6       TCGA-D3-A2J7 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2J8       TCGA-D3-A2J9       TCGA-D3-A2JA       TCGA-D3-A2JB 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2JC       TCGA-D3-A2JD       TCGA-D3-A2JG       TCGA-D3-A2JH 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2JK       TCGA-D3-A2JL       TCGA-D3-A2JN       TCGA-D3-A2JO 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2JP       TCGA-D3-A3BZ       TCGA-D3-A3C1       TCGA-D3-A3C3 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A3C6       TCGA-D3-A3C7       TCGA-D3-A3CB       TCGA-D3-A3CC 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A3CE       TCGA-D3-A3CF       TCGA-D3-A3MO       TCGA-D3-A3MR 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A3MU       TCGA-D3-A3MV       TCGA-D3-A51E       TCGA-D3-A51F 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A51H       TCGA-D3-A51J       TCGA-D3-A51K       TCGA-D3-A51N 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A51R       TCGA-D3-A51T       TCGA-D3-A5GL       TCGA-D3-A5GN 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A5GO       TCGA-D3-A5GR       TCGA-D3-A5GS       TCGA-D3-A5GU 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D9-A3Z1       TCGA-D9-A3Z3       TCGA-D9-A6E9       TCGA-D9-A6EA 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D9-A6EC       TCGA-D9-A6EG       TCGA-DA-A1HV       TCGA-DA-A1HW 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1HY       TCGA-DA-A1I0       TCGA-DA-A1I1       TCGA-DA-A1I2 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1I4       TCGA-DA-A1I5       TCGA-DA-A1I7       TCGA-DA-A1I8 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1IA       TCGA-DA-A1IB       TCGA-DA-A1IC       TCGA-DA-A3F2 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A3F3       TCGA-DA-A3F5       TCGA-DA-A3F8       TCGA-EB-A44Q 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EB-A44R       TCGA-EB-A5KH       TCGA-EB-A5UL       TCGA-EB-A5UN 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EB-A5VV       TCGA-EB-A6L9       TCGA-EE-A17X       TCGA-EE-A17Y 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A17Z       TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A183 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A20B       TCGA-EE-A20C       TCGA-EE-A20F 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A20I       TCGA-EE-A29A       TCGA-EE-A29B       TCGA-EE-A29C 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29D       TCGA-EE-A29E       TCGA-EE-A29G       TCGA-EE-A29H 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29M       TCGA-EE-A29N       TCGA-EE-A29P       TCGA-EE-A29Q 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29R       TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29W 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A0       TCGA-EE-A2A1       TCGA-EE-A2A2 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2A5       TCGA-EE-A2A6       TCGA-EE-A2GB       TCGA-EE-A2GC 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GE       TCGA-EE-A2GH       TCGA-EE-A2GI       TCGA-EE-A2GJ 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GK       TCGA-EE-A2GL       TCGA-EE-A2GM       TCGA-EE-A2GN 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GP       TCGA-EE-A2GR       TCGA-EE-A2GS       TCGA-EE-A2GT 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GU       TCGA-EE-A2M5       TCGA-EE-A2M6       TCGA-EE-A2M7 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2M8       TCGA-EE-A2MC       TCGA-EE-A2MD       TCGA-EE-A2ME 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MF       TCGA-EE-A2MG       TCGA-EE-A2MH       TCGA-EE-A2MI 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MJ       TCGA-EE-A2MK       TCGA-EE-A2ML       TCGA-EE-A2MM 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MN       TCGA-EE-A2MP       TCGA-EE-A2MQ       TCGA-EE-A2MS 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MT       TCGA-EE-A2MU       TCGA-EE-A3AA       TCGA-EE-A3AB 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3AC       TCGA-EE-A3AD       TCGA-EE-A3AE       TCGA-EE-A3AF 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3AG       TCGA-EE-A3AH       TCGA-EE-A3J3       TCGA-EE-A3J4 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3J5       TCGA-EE-A3J7       TCGA-EE-A3J8       TCGA-EE-A3JA 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3JB       TCGA-EE-A3JE       TCGA-EE-A3JH       TCGA-ER-A197 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A199       TCGA-ER-A19A       TCGA-ER-A19C       TCGA-ER-A19D 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A19E       TCGA-ER-A19J       TCGA-ER-A19M       TCGA-ER-A19O 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A19T       TCGA-ER-A1A1       TCGA-ER-A2NC       TCGA-ER-A2ND 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A2NE       TCGA-ER-A2NF       TCGA-ER-A2NG       TCGA-ER-A2NH 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A3ET       TCGA-ER-A3EV       TCGA-ER-A3PL       TCGA-ER-A42K 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A42L       TCGA-FR-A3YN       TCGA-FR-A44A       TCGA-FR-A69P 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1YW       TCGA-FS-A1YX       TCGA-FS-A1YY       TCGA-FS-A1Z0 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1Z3       TCGA-FS-A1Z4       TCGA-FS-A1Z7       TCGA-FS-A1ZA 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZB       TCGA-FS-A1ZC       TCGA-FS-A1ZD       TCGA-FS-A1ZE 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZG       TCGA-FS-A1ZH       TCGA-FS-A1ZJ       TCGA-FS-A1ZK 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZM       TCGA-FS-A1ZP       TCGA-FS-A1ZQ       TCGA-FS-A1ZR 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZS       TCGA-FS-A1ZT       TCGA-FS-A1ZU       TCGA-FS-A1ZW 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZY       TCGA-FS-A1ZZ       TCGA-FS-A4F0       TCGA-FS-A4F4 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A4F5       TCGA-FS-A4F8       TCGA-FS-A4F9       TCGA-FS-A4FB 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A4FC       TCGA-FS-A4FD       TCGA-FW-A3I3       TCGA-FW-A3TV 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FW-A5DY       TCGA-GF-A3OT       TCGA-GF-A4EO       TCGA-GF-A6C8 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GF-A6C9       TCGA-GN-A267       TCGA-GN-A268       TCGA-GN-A26A 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GN-A26D       TCGA-GN-A4U3       TCGA-GN-A4U4       TCGA-GN-A4U7 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GN-A4U9       TCGA-QB-A6FS       TCGA-RP-A693       TCGA-RP-A694 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-RP-A695 
"ZNF589 WILD-TYPE" 
                  vv
clus               T0+T1 T2 T3 T4
  ZNF589 MUTATED       1  1  0  0
  ZNF589 WILD-TYPE    52 61 60 55
D79V5, multiclass
[1] "Remove cluster labels:" "ZNF589 MUTATED"        
clus
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               2              228 
      TCGA-D3-A2JF       TCGA-D3-A3ML       TCGA-EB-A5SH       TCGA-EE-A180 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A184       TCGA-EE-A20H       TCGA-EE-A29L       TCGA-EE-A2GD 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GO       TCGA-EE-A2MR       TCGA-ER-A193       TCGA-FR-A3YO 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZF       TCGA-D3-A1Q1       TCGA-D3-A1Q3       TCGA-D3-A1Q4 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A1Q6       TCGA-D3-A1Q7       TCGA-D3-A1Q8       TCGA-D3-A1Q9 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A1QA       TCGA-D3-A1QB       TCGA-D3-A2J6       TCGA-D3-A2J7 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2J8       TCGA-D3-A2J9       TCGA-D3-A2JA       TCGA-D3-A2JC 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2JD       TCGA-D3-A2JG       TCGA-D3-A2JH       TCGA-D3-A2JK 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2JN       TCGA-D3-A2JP       TCGA-D3-A3BZ       TCGA-D3-A3C6 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A3C7       TCGA-D3-A3CB       TCGA-D3-A3CC       TCGA-D3-A3CE 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A3CF       TCGA-D3-A3MR       TCGA-D3-A3MU       TCGA-D3-A3MV 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A51E       TCGA-D3-A51F       TCGA-D3-A51H       TCGA-D3-A51J 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A51N       TCGA-D3-A51R       TCGA-D3-A51T       TCGA-D3-A5GL 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A5GN       TCGA-D3-A5GO       TCGA-D3-A5GR       TCGA-D3-A5GS 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A5GU       TCGA-D9-A3Z1       TCGA-D9-A3Z3       TCGA-D9-A6E9 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D9-A6EA       TCGA-D9-A6EC       TCGA-D9-A6EG       TCGA-DA-A1HV 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1HW       TCGA-DA-A1HY       TCGA-DA-A1I0       TCGA-DA-A1I1 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1I2       TCGA-DA-A1I4       TCGA-DA-A1I5       TCGA-DA-A1I7 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1I8       TCGA-DA-A1IA       TCGA-DA-A1IB       TCGA-DA-A1IC 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A3F2       TCGA-DA-A3F3       TCGA-DA-A3F5       TCGA-DA-A3F8 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EB-A5KH       TCGA-EB-A5UN       TCGA-EB-A5VV       TCGA-EE-A17X 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A17Y       TCGA-EE-A17Z       TCGA-EE-A181       TCGA-EE-A182 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A20B       TCGA-EE-A20F       TCGA-EE-A29A 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29B       TCGA-EE-A29C       TCGA-EE-A29D       TCGA-EE-A29E 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29G       TCGA-EE-A29H       TCGA-EE-A29M       TCGA-EE-A29P 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S       TCGA-EE-A29V 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A0       TCGA-EE-A2A1       TCGA-EE-A2A2 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2A5       TCGA-EE-A2A6       TCGA-EE-A2GB       TCGA-EE-A2GC 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GE       TCGA-EE-A2GH       TCGA-EE-A2GI       TCGA-EE-A2GJ 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GK       TCGA-EE-A2GL       TCGA-EE-A2GM       TCGA-EE-A2GN 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GP       TCGA-EE-A2GR       TCGA-EE-A2GS       TCGA-EE-A2GT 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GU       TCGA-EE-A2M5       TCGA-EE-A2M6       TCGA-EE-A2M7 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2M8       TCGA-EE-A2MC       TCGA-EE-A2MD       TCGA-EE-A2ME 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MF       TCGA-EE-A2MG       TCGA-EE-A2MH       TCGA-EE-A2MI 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MJ       TCGA-EE-A2MK       TCGA-EE-A2ML       TCGA-EE-A2MM 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MN       TCGA-EE-A2MP       TCGA-EE-A2MQ       TCGA-EE-A2MS 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MT       TCGA-EE-A2MU       TCGA-EE-A3AA       TCGA-EE-A3AB 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3AC       TCGA-EE-A3AD       TCGA-EE-A3AE       TCGA-EE-A3AF 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3AG       TCGA-EE-A3AH       TCGA-EE-A3J3       TCGA-EE-A3J4 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3J5       TCGA-EE-A3J7       TCGA-EE-A3J8       TCGA-EE-A3JA 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3JB       TCGA-EE-A3JE       TCGA-EE-A3JH       TCGA-ER-A197 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A199       TCGA-ER-A19C       TCGA-ER-A19D       TCGA-ER-A19E 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A19M       TCGA-ER-A19O       TCGA-ER-A19T       TCGA-ER-A2NC 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A2ND       TCGA-ER-A2NF       TCGA-ER-A2NG       TCGA-ER-A2NH 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A3ET       TCGA-ER-A3EV       TCGA-ER-A3PL       TCGA-ER-A42K 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A42L       TCGA-FR-A3YN       TCGA-FR-A44A       TCGA-FS-A1YW 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1YX       TCGA-FS-A1YY       TCGA-FS-A1Z0       TCGA-FS-A1Z4 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1Z7       TCGA-FS-A1ZA       TCGA-FS-A1ZB       TCGA-FS-A1ZD 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZE       TCGA-FS-A1ZG       TCGA-FS-A1ZH       TCGA-FS-A1ZJ 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZK       TCGA-FS-A1ZM       TCGA-FS-A1ZP       TCGA-FS-A1ZR 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZS       TCGA-FS-A1ZT       TCGA-FS-A1ZU       TCGA-FS-A1ZW 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZY       TCGA-FS-A1ZZ       TCGA-FS-A4F0       TCGA-FS-A4F4 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A4F5       TCGA-FS-A4F8       TCGA-FS-A4F9       TCGA-FS-A4FB 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A4FC       TCGA-FS-A4FD       TCGA-FW-A3TV       TCGA-FW-A5DY 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GF-A3OT       TCGA-GF-A4EO       TCGA-GF-A6C8       TCGA-GN-A267 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GN-A268       TCGA-GN-A26A       TCGA-GN-A26D       TCGA-GN-A4U3 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GN-A4U4       TCGA-GN-A4U7       TCGA-GN-A4U9       TCGA-QB-A6FS 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
                  vv
clus                N0  N1  N2  N3
  ZNF589 MUTATED     1   0   2   0
  ZNF589 WILD-TYPE 142  53  32  35
D79V6, multiclass
    clus
vv   ZNF589 MUTATED ZNF589 WILD-TYPE
  N0              1              142
  N1              0               53
  N2              2               32
  N3              0               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"
D79V7, binary
                  cls
clus                 0   1
  ZNF589 MUTATED     3   0
  ZNF589 WILD-TYPE 253  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF589 MUTATED      3    0
  ZNF589 WILD-TYPE  253   17
   clus
vv  ZNF589 MUTATED ZNF589 WILD-TYPE
  0              3              253
  1              0               17
[1] 2 2
[1] FALSE
D79V8, binary
                  cls
clus                 0   1
  ZNF589 MUTATED     2   0
  ZNF589 WILD-TYPE 105  73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF589 MUTATED      2    0
  ZNF589 WILD-TYPE  105   73
     clus
vv    ZNF589 MUTATED ZNF589 WILD-TYPE
  NO               2              105
  YES              0               73
[1] 2 2
[1] FALSE
D79V9, binary
                  cls
clus                 0   1
  ZNF589 MUTATED     1   2
  ZNF589 WILD-TYPE  36 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF589 MUTATED      1    2
  ZNF589 WILD-TYPE   36  251
     clus
vv    ZNF589 MUTATED ZNF589 WILD-TYPE
  NO               1               36
  YES              2              251
[1] 2 2
[1] FALSE
D79V10, continuous
[1] "Remove cluster labels:" "ZNF589 MUTATED"        
clus
  ZNF589 MUTATED ZNF589 WILD-TYPE 
               1              211 
      TCGA-D3-A2JF       TCGA-D3-A3ML       TCGA-D3-A51G       TCGA-EB-A5SH 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A180       TCGA-EE-A184       TCGA-EE-A20H       TCGA-EE-A29L 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GD       TCGA-EE-A2GO       TCGA-EE-A2MR       TCGA-ER-A198 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZF       TCGA-D3-A1Q1       TCGA-D3-A1Q3       TCGA-D3-A1Q4 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A1Q6       TCGA-D3-A1Q7       TCGA-D3-A1Q9       TCGA-D3-A1QA 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2J6       TCGA-D3-A2J7       TCGA-D3-A2J8       TCGA-D3-A2J9 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2JA       TCGA-D3-A2JD       TCGA-D3-A2JG       TCGA-D3-A2JH 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A2JK       TCGA-D3-A3BZ       TCGA-D3-A3C6       TCGA-D3-A3CB 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A3CC       TCGA-D3-A3CF       TCGA-D3-A3MU       TCGA-D3-A3MV 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A51E       TCGA-D3-A51F       TCGA-D3-A51H       TCGA-D3-A51K 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A51R       TCGA-D3-A51T       TCGA-D3-A5GL       TCGA-D3-A5GN 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D3-A5GO       TCGA-D3-A5GR       TCGA-D3-A5GS       TCGA-D3-A5GU 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D9-A3Z1       TCGA-D9-A3Z3       TCGA-D9-A6E9       TCGA-D9-A6EA 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-D9-A6EC       TCGA-D9-A6EG       TCGA-DA-A1HW       TCGA-DA-A1HY 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1I0       TCGA-DA-A1I4       TCGA-DA-A1I5       TCGA-DA-A1I8 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A1IA       TCGA-DA-A1IB       TCGA-DA-A1IC       TCGA-DA-A3F2 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-DA-A3F5       TCGA-DA-A3F8       TCGA-EB-A5UL       TCGA-EB-A5UN 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EB-A5VV       TCGA-EE-A17X       TCGA-EE-A17Y       TCGA-EE-A17Z 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A185       TCGA-EE-A20B 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A20F       TCGA-EE-A29A       TCGA-EE-A29B       TCGA-EE-A29C 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29D       TCGA-EE-A29E       TCGA-EE-A29G       TCGA-EE-A29H 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29M       TCGA-EE-A29P       TCGA-EE-A29Q       TCGA-EE-A29R 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29W       TCGA-EE-A29X 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2A0       TCGA-EE-A2A1       TCGA-EE-A2A2       TCGA-EE-A2A5 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2A6       TCGA-EE-A2GB       TCGA-EE-A2GC       TCGA-EE-A2GE 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GH       TCGA-EE-A2GI       TCGA-EE-A2GJ       TCGA-EE-A2GK 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GL       TCGA-EE-A2GM       TCGA-EE-A2GN       TCGA-EE-A2GP 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2GR       TCGA-EE-A2GS       TCGA-EE-A2GT       TCGA-EE-A2GU 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2M5       TCGA-EE-A2M6       TCGA-EE-A2M7       TCGA-EE-A2M8 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MC       TCGA-EE-A2MD       TCGA-EE-A2ME       TCGA-EE-A2MF 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MG       TCGA-EE-A2MH       TCGA-EE-A2MI       TCGA-EE-A2MJ 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MK       TCGA-EE-A2ML       TCGA-EE-A2MM       TCGA-EE-A2MN 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MP       TCGA-EE-A2MQ       TCGA-EE-A2MS       TCGA-EE-A2MT 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A2MU       TCGA-EE-A3AE       TCGA-EE-A3AH       TCGA-EE-A3J3 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3J4       TCGA-EE-A3J5       TCGA-EE-A3J7       TCGA-EE-A3J8 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-EE-A3JA       TCGA-EE-A3JB       TCGA-EE-A3JE       TCGA-EE-A3JH 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A197       TCGA-ER-A199       TCGA-ER-A19C       TCGA-ER-A19D 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A19E       TCGA-ER-A19F       TCGA-ER-A19G       TCGA-ER-A19H 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A19M       TCGA-ER-A19Q       TCGA-ER-A19T       TCGA-ER-A19W 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A2NC       TCGA-ER-A2ND       TCGA-ER-A2NF       TCGA-ER-A2NG 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A2NH       TCGA-ER-A3ET       TCGA-ER-A3EV       TCGA-ER-A3PL 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-ER-A42K       TCGA-ER-A42L       TCGA-FR-A3YN       TCGA-FR-A44A 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1YW       TCGA-FS-A1YX       TCGA-FS-A1YY       TCGA-FS-A1Z0 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1Z4       TCGA-FS-A1Z7       TCGA-FS-A1ZA       TCGA-FS-A1ZB 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZD       TCGA-FS-A1ZE       TCGA-FS-A1ZG       TCGA-FS-A1ZH 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZJ       TCGA-FS-A1ZK       TCGA-FS-A1ZM       TCGA-FS-A1ZP 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZR       TCGA-FS-A1ZS       TCGA-FS-A1ZT       TCGA-FS-A1ZU 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A1ZW       TCGA-FS-A1ZY       TCGA-FS-A1ZZ       TCGA-FS-A4F0 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A4F4       TCGA-FS-A4F5       TCGA-FS-A4F8       TCGA-FS-A4F9 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-FS-A4FB       TCGA-FS-A4FC       TCGA-FS-A4FD       TCGA-FW-A3TV 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GF-A6C8       TCGA-GN-A262       TCGA-GN-A264       TCGA-GN-A267 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GN-A268       TCGA-GN-A26A       TCGA-GN-A26D       TCGA-GN-A4U3 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
      TCGA-GN-A4U4       TCGA-GN-A4U7       TCGA-GN-A4U9 
"ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" "ZNF589 WILD-TYPE" 
D79V11, binary
                  cls
clus                 0   1
  ZNF589 MUTATED     0   3
  ZNF589 WILD-TYPE 109 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF589 MUTATED      0    3
  ZNF589 WILD-TYPE  109  178
        clus
vv       ZNF589 MUTATED ZNF589 WILD-TYPE
  FEMALE              0              109
  MALE                3              178
[1] 2 2
[1] FALSE
D79V12, binary
                  cls
clus                 0   1
  ZNF589 MUTATED     2   1
  ZNF589 WILD-TYPE 252  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF589 MUTATED      2    1
  ZNF589 WILD-TYPE  252   34
     clus
vv    ZNF589 MUTATED ZNF589 WILD-TYPE
  NO               2              252
  YES              1               34
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF589 MUTATED       0                         0     3
  ZNF589 WILD-TYPE     5                         1   281
D79V13, multiclass
                           clus
vv                          ZNF589 MUTATED ZNF589 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  3              281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                  cls
clus                 0   1
  ZNF589 MUTATED     0   3
  ZNF589 WILD-TYPE   3 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF589 MUTATED      0    3
  ZNF589 WILD-TYPE    3  280
                        clus
vv                       ZNF589 MUTATED ZNF589 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              280
[1] 2 2
[1] FALSE

Clustering(80) Variable = DSP MUTATION ANALYSIS
D80V1, survival
               sevent
clus2            0  1
  DSP MUTATED   20 22
  DSP WILD-TYPE 77 81
  DSP MUTATED DSP WILD-TYPE 
           42           158 
  DSP MUTATED DSP WILD-TYPE 
           22            81 
$`DSP MUTATED`
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 
       62.07       166.75       269.03       134.40        19.04        36.85 
TCGA-D3-A2J8 TCGA-D3-A2JH TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
       62.86        36.30        11.34        69.21        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       68.68       110.53        42.64        13.15        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M 
       26.24        75.55        76.14        12.99         0.26        47.74 
TCGA-EE-A2A2 TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MP 
       30.02        32.48         0.76       209.79        63.25       227.01 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-ER-A19W 
      143.93        64.04        54.51         6.28         3.35       146.63 
TCGA-ER-A42L TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-GN-A267 
       74.47       195.98         8.35       130.95         3.06        17.06 

$`DSP WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-EE-A3JD TCGA-D3-A1Q1 
       38.76        33.24        31.96        52.90        27.35         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB 
       76.41        62.60        25.64        45.99        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       86.30       107.61       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       62.70        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EG TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
       22.85       150.61        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
      225.11         3.91        16.41        52.41        18.21        24.89 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       79.20        75.22        44.28        47.41        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      346.49       185.19       115.43        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
      201.60        68.65        10.62        18.35        93.63         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
       94.19       171.85        89.26       104.78       145.45        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J4 
       53.26       124.31       122.73         4.41        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       45.90       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        32.05         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      174.21       171.78        49.74        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT 
       43.92         7.82        36.33        78.61       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       18.25         1.91        53.29       117.93        96.92        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  DSP MUTATED DSP WILD-TYPE 
          0.0           0.2 
  DSP MUTATED DSP WILD-TYPE 
       269.03        346.49 
  DSP MUTATED DSP WILD-TYPE 
       58.290        46.455 
[1] "0.0 - 269.0 (58.3)" "0.2 - 346.5 (46.5)"
[1] "hr=" "1"  
D80V2, survival
               sevent
clus2             0   1
  DSP MUTATED    24  34
  DSP WILD-TYPE 100 126
  DSP MUTATED DSP WILD-TYPE 
           58           226 
  DSP MUTATED DSP WILD-TYPE 
           34           126 
$`DSP MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        13.87       168.26         2.60       340.14       134.40 
TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A51T 
       31.40        36.95        65.49        11.87        42.08        26.89 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F8 
       77.56        76.57       144.89       222.51       135.02        43.36 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C 
       29.82        33.73        14.70        26.89       151.27        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2A2 TCGA-EE-A2GC 
       13.97        63.78        56.84        18.61        59.64        67.43 
TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MF 
       48.72        79.66        13.91        21.67        47.28       268.73 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       96.23       248.65       162.48        64.04        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-ER-A19W TCGA-ER-A42L TCGA-FR-A69P 
       41.59        34.32        53.19       148.18       149.03        15.72 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZR 
      202.65        20.91        27.72        23.93       133.55        11.41 
TCGA-FS-A1ZZ TCGA-FS-A4FC TCGA-GF-A6C9 TCGA-GN-A267 
       27.02        54.41        15.78        64.44 

$`DSP WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A2GO 
       46.32        68.25        54.02        94.98        68.15       126.81 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       27.35        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74        43.43       103.10        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.76       113.52        12.10       171.58        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 
       22.29         9.90        25.18        22.95        36.03        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        33.93        10.49       225.96        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       20.35        29.29        58.92         7.04        36.46        27.22 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        8.65         4.96       133.81        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       85.08        72.07        64.64        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.96        39.29        86.14        59.28       173.79       220.24 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
      107.38        54.74        75.48       102.12        42.77        81.21 
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-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        47.54        43.23        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
      122.73        28.77       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       64.08       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 
       92.98       174.21       216.92        48.59       228.59        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        48.85       357.37        53.52        46.45         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        34.03        26.73        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.51        19.30         9.90        19.43         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        10.13        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  DSP MUTATED DSP WILD-TYPE 
          2.6           0.2 
  DSP MUTATED DSP WILD-TYPE 
       340.14        369.93 
  DSP MUTATED DSP WILD-TYPE 
        53.80         53.97 
[1] "2.6 - 340.1 (53.8)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1"  
D80V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DSP MUTATED          2       3       5        5        5        6         2
  DSP WILD-TYPE        8       3      20        5       20       12         8
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DSP MUTATED           4         0         6          4          6          8
  DSP WILD-TYPE        10        10        30         10         20         35
               vv
clus            STAGE IV
  DSP MUTATED          3
  DSP WILD-TYPE       13
D80V4, multiclass
            clus
vv           DSP MUTATED DSP WILD-TYPE
  I/II NOS             2             8
  STAGE 0              3             3
  STAGE I              5            20
  STAGE IA             5             5
  STAGE IB             5            20
  STAGE II             6            12
  STAGE IIA            2             8
  STAGE IIB            4            10
  STAGE IIC            0            10
  STAGE III            6            30
  STAGE IIIA           4            10
  STAGE IIIB           6            20
  STAGE IIIC           8            35
  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 12
  DSP WILD-TYPE    41 50 47 43
D80V5, multiclass
       clus
vv      DSP MUTATED DSP WILD-TYPE
  T0+T1          12            41
  T2             12            50
  T3             13            47
  T4             12            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  DSP MUTATED    35  11   8   3
  DSP WILD-TYPE 108  42  26  32
D80V6, multiclass
    clus
vv   DSP MUTATED DSP WILD-TYPE
  N0          35           108
  N1          11            42
  N2           8            26
  N3           3            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"
D80V7, binary
               cls
clus              0   1
  DSP MUTATED    54   3
  DSP WILD-TYPE 202  14
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     54    3
  DSP WILD-TYPE  202   14
   clus
vv  DSP MUTATED DSP WILD-TYPE
  0          54           202
  1           3            14
[1] 2 2
[1] FALSE
D80V8, binary
               cls
clus             0  1
  DSP MUTATED   26 13
  DSP WILD-TYPE 81 60
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     26   13
  DSP WILD-TYPE   81   60
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO           26            81
  YES          13            60
[1] 2 2
[1] FALSE
D80V9, binary
               cls
clus              0   1
  DSP MUTATED     8  52
  DSP WILD-TYPE  29 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      8   52
  DSP WILD-TYPE   29  201
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO            8            29
  YES          52           201
[1] 2 2
[1] FALSE
D80V10, continuous
D80V11, binary
               cls
clus              0   1
  DSP MUTATED    19  41
  DSP WILD-TYPE  90 140
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     19   41
  DSP WILD-TYPE   90  140
        clus
vv       DSP MUTATED DSP WILD-TYPE
  FEMALE          19            90
  MALE            41           140
[1] 2 2
[1] FALSE
D80V12, binary
               cls
clus              0   1
  DSP MUTATED    52   8
  DSP WILD-TYPE 202  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED     52    8
  DSP WILD-TYPE  202   27
     clus
vv    DSP MUTATED DSP WILD-TYPE
  NO           52           202
  YES           8            27
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSP MUTATED       0                         0    60
  DSP WILD-TYPE     5                         1   224
D80V13, multiclass
                           clus
vv                          DSP MUTATED DSP WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              60           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"
D80V14, binary
               cls
clus              0   1
  DSP MUTATED     1  58
  DSP WILD-TYPE   2 225
[1] "tbl2"
               cls
clus            [,1] [,2]
  DSP MUTATED      1   58
  DSP WILD-TYPE    2  225
                        clus
vv                       DSP MUTATED DSP WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          58           225
[1] 2 2
[1] FALSE

Clustering(81) Variable = ZZZ3 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  ZZZ3 MUTATED     1   2
  ZZZ3 WILD-TYPE  96 101
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
             3            197 
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
             2            101 
$`ZZZ3 MUTATED`
TCGA-D9-A6EC TCGA-EE-A182 TCGA-GN-A26A 
       69.21         0.00         7.59 

$`ZZZ3 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        15.02        22.29        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        24.89        20.38        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      104.78       145.45       227.01       143.93        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04         4.41        54.51         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      135.98        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        96.92        17.06        42.48       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
           0.0            0.2 
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
         69.21         346.49 
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
          7.59          47.41 
[1] "0.0 - 69.2 (7.6)"   "0.2 - 346.5 (47.4)"
[1] "hr=" "3.2"
D81V2, survival
                sevent
clus2              0   1
  ZZZ3 MUTATED     1   2
  ZZZ3 WILD-TYPE 123 158
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
             3            281 
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
             2            158 
$`ZZZ3 MUTATED`
TCGA-D9-A6EC TCGA-EE-A182 TCGA-GN-A26A 
       77.56        14.70        32.48 

$`ZZZ3 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29         9.90        25.18        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        8.65        33.73        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
          14.7            0.2 
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
         77.56         369.93 
  ZZZ3 MUTATED ZZZ3 WILD-TYPE 
         32.48          54.02 
[1] "14.7 - 77.6 (32.5)" "0.2 - 369.9 (54.0)"
[1] "hr=" "2"  
D81V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ZZZ3 MUTATED          0       0       0        0        0        0         0
  ZZZ3 WILD-TYPE       10       6      25       10       25       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZZZ3 MUTATED           0         0         0          2          0          1
  ZZZ3 WILD-TYPE        14        10        36         12         26         42
                vv
clus             STAGE IV
  ZZZ3 MUTATED          0
  ZZZ3 WILD-TYPE       16
D81V4, multiclass
            clus
vv           ZZZ3 MUTATED ZZZ3 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               0             25
  STAGE IA              0             10
  STAGE IB              0             25
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             0             14
  STAGE IIC             0             10
  STAGE III             0             36
  STAGE IIIA            2             12
  STAGE IIIB            0             26
  STAGE IIIC            1             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
  ZZZ3 MUTATED       0  0  2  1
  ZZZ3 WILD-TYPE    53 62 58 54
D81V5, multiclass
       clus
vv      ZZZ3 MUTATED ZZZ3 WILD-TYPE
  T0+T1            0             53
  T2               0             62
  T3               2             58
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ZZZ3 MUTATED     0   3   0   0
  ZZZ3 WILD-TYPE 143  50  34  35
D81V6, multiclass
    clus
vv   ZZZ3 MUTATED ZZZ3 WILD-TYPE
  N0            0            143
  N1            3             50
  N2            0             34
  N3            0             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"
D81V7, binary
                cls
clus               0   1
  ZZZ3 MUTATED     3   0
  ZZZ3 WILD-TYPE 253  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZZZ3 MUTATED      3    0
  ZZZ3 WILD-TYPE  253   17
   clus
vv  ZZZ3 MUTATED ZZZ3 WILD-TYPE
  0            3            253
  1            0             17
[1] 2 2
[1] FALSE
D81V8, binary
                cls
clus               0   1
  ZZZ3 MUTATED     2   1
  ZZZ3 WILD-TYPE 105  72
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZZZ3 MUTATED      2    1
  ZZZ3 WILD-TYPE  105   72
     clus
vv    ZZZ3 MUTATED ZZZ3 WILD-TYPE
  NO             2            105
  YES            1             72
[1] 2 2
[1] FALSE
D81V9, binary
                cls
clus               0   1
  ZZZ3 MUTATED     0   3
  ZZZ3 WILD-TYPE  37 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZZZ3 MUTATED      0    3
  ZZZ3 WILD-TYPE   37  250
     clus
vv    ZZZ3 MUTATED ZZZ3 WILD-TYPE
  NO             0             37
  YES            3            250
[1] 2 2
[1] FALSE
D81V10, continuous
D81V11, binary
                cls
clus               0   1
  ZZZ3 MUTATED     2   1
  ZZZ3 WILD-TYPE 107 180
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZZZ3 MUTATED      2    1
  ZZZ3 WILD-TYPE  107  180
        clus
vv       ZZZ3 MUTATED ZZZ3 WILD-TYPE
  FEMALE            2            107
  MALE              1            180
[1] 2 2
[1] FALSE
D81V12, binary
                cls
clus               0   1
  ZZZ3 MUTATED     3   0
  ZZZ3 WILD-TYPE 251  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZZZ3 MUTATED      3    0
  ZZZ3 WILD-TYPE  251   35
     clus
vv    ZZZ3 MUTATED ZZZ3 WILD-TYPE
  NO             3            251
  YES            0             35
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZZZ3 MUTATED       0                         0     3
  ZZZ3 WILD-TYPE     5                         1   281
D81V13, multiclass
                           clus
vv                          ZZZ3 MUTATED ZZZ3 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3            281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                cls
clus               0   1
  ZZZ3 MUTATED     0   3
  ZZZ3 WILD-TYPE   3 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZZZ3 MUTATED      0    3
  ZZZ3 WILD-TYPE    3  280
                        clus
vv                       ZZZ3 MUTATED ZZZ3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            280
[1] 2 2
[1] FALSE

Clustering(82) Variable = MCART2 MUTATION ANALYSIS
D82V1, survival
                  sevent
clus2               0  1
  MCART2 MUTATED    3  5
  MCART2 WILD-TYPE 94 98
  MCART2 MUTATED MCART2 WILD-TYPE 
               8              192 
  MCART2 MUTATED MCART2 WILD-TYPE 
               5               98 
$`MCART2 MUTATED`
TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-EE-A181 TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GJ 
       27.35        36.85        20.38        30.02        12.95        68.65 
TCGA-EE-A2GS TCGA-OD-A75X 
       71.31       297.01 

$`MCART2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90       134.40        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        24.89         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       77.98        26.14       201.60        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.76         0.20        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      120.53        34.49        46.92         7.23         0.20         0.33 

  MCART2 MUTATED MCART2 WILD-TYPE 
           12.95             0.00 
  MCART2 MUTATED MCART2 WILD-TYPE 
          297.01           346.49 
  MCART2 MUTATED MCART2 WILD-TYPE 
          33.435           47.575 
[1] "12.9 - 297.0 (33.4)" "0.0 - 346.5 (47.6)" 
[1] "hr=" "1.1"
D82V2, survival
                  sevent
clus2                0   1
  MCART2 MUTATED     3   7
  MCART2 WILD-TYPE 121 153
  MCART2 MUTATED MCART2 WILD-TYPE 
              10              274 
  MCART2 MUTATED MCART2 WILD-TYPE 
               7              153 
$`MCART2 MUTATED`
TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-EE-A181 TCGA-EE-A2A2 TCGA-EE-A2GE TCGA-EE-A2GJ 
       27.35        36.95        33.73        59.64       173.79       107.38 
TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-FS-A4FC TCGA-OD-A75X 
       81.21        21.67        54.41       297.90 

$`MCART2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        39.29        86.14        59.28        67.43 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24        48.72        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        42.77        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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-A3TU TCGA-FW-A3TV 
       34.03        26.73        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  MCART2 MUTATED MCART2 WILD-TYPE 
           21.67             0.20 
  MCART2 MUTATED MCART2 WILD-TYPE 
          297.90           369.93 
  MCART2 MUTATED MCART2 WILD-TYPE 
          57.025           53.720 
[1] "21.7 - 297.9 (57.0)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1"  
D82V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MCART2 MUTATED          0       0       2        1        1        1
  MCART2 WILD-TYPE       10       6      23        9       24       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MCART2 MUTATED           1         0         0         2          0
  MCART2 WILD-TYPE         9        14        10        34         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MCART2 MUTATED            0          1        0
  MCART2 WILD-TYPE         26         42       16
D82V4, multiclass
            clus
vv           MCART2 MUTATED MCART2 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 2               23
  STAGE IA                1                9
  STAGE IB                1               24
  STAGE II                1               17
  STAGE IIA               1                9
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               2               34
  STAGE IIIA              0               14
  STAGE IIIB              0               26
  STAGE IIIC              1               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
  MCART2 MUTATED       1  3  2  1
  MCART2 WILD-TYPE    52 59 58 54
D82V5, multiclass
       clus
vv      MCART2 MUTATED MCART2 WILD-TYPE
  T0+T1              1               52
  T2                 3               59
  T3                 2               58
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MCART2 MUTATED     6   1   2   0
  MCART2 WILD-TYPE 137  52  32  35
D82V6, multiclass
    clus
vv   MCART2 MUTATED MCART2 WILD-TYPE
  N0              6              137
  N1              1               52
  N2              2               32
  N3              0               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"
D82V7, binary
                  cls
clus                 0   1
  MCART2 MUTATED    10   0
  MCART2 WILD-TYPE 246  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART2 MUTATED     10    0
  MCART2 WILD-TYPE  246   17
   clus
vv  MCART2 MUTATED MCART2 WILD-TYPE
  0             10              246
  1              0               17
[1] 2 2
[1] FALSE
D82V8, binary
                  cls
clus                 0   1
  MCART2 MUTATED     5   1
  MCART2 WILD-TYPE 102  72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART2 MUTATED      5    1
  MCART2 WILD-TYPE  102   72
     clus
vv    MCART2 MUTATED MCART2 WILD-TYPE
  NO               5              102
  YES              1               72
[1] 2 2
[1] FALSE
D82V9, binary
                  cls
clus                 0   1
  MCART2 MUTATED     1   9
  MCART2 WILD-TYPE  36 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART2 MUTATED      1    9
  MCART2 WILD-TYPE   36  244
     clus
vv    MCART2 MUTATED MCART2 WILD-TYPE
  NO               1               36
  YES              9              244
[1] 2 2
[1] FALSE
D82V10, continuous
D82V11, binary
                  cls
clus                 0   1
  MCART2 MUTATED     3   7
  MCART2 WILD-TYPE 106 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART2 MUTATED      3    7
  MCART2 WILD-TYPE  106  174
        clus
vv       MCART2 MUTATED MCART2 WILD-TYPE
  FEMALE              3              106
  MALE                7              174
[1] 2 2
[1] FALSE
D82V12, binary
                  cls
clus                 0   1
  MCART2 MUTATED     9   1
  MCART2 WILD-TYPE 245  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART2 MUTATED      9    1
  MCART2 WILD-TYPE  245   34
     clus
vv    MCART2 MUTATED MCART2 WILD-TYPE
  NO               9              245
  YES              1               34
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MCART2 MUTATED       0                         0    10
  MCART2 WILD-TYPE     5                         1   274
D82V13, multiclass
                           clus
vv                          MCART2 MUTATED MCART2 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 10              274
[1] 3 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
  MCART2 MUTATED     0  10
  MCART2 WILD-TYPE   3 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART2 MUTATED      0   10
  MCART2 WILD-TYPE    3  273
                        clus
vv                       MCART2 MUTATED MCART2 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              273
[1] 2 2
[1] FALSE

Clustering(83) Variable = CD2 MUTATION ANALYSIS
D83V1, survival
               sevent
clus2            0  1
  CD2 MUTATED   12  6
  CD2 WILD-TYPE 85 97
  CD2 MUTATED CD2 WILD-TYPE 
           18           182 
  CD2 MUTATED CD2 WILD-TYPE 
            6            97 
$`CD2 MUTATED`
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A51R TCGA-D3-A5GN 
       52.90        27.35        36.85        76.41        62.70        45.70 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2GM 
       20.38        12.99         0.26        47.74        27.16        18.35 
TCGA-EE-A2GP TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MS TCGA-ER-A42L 
        0.76       209.79        63.25       227.01       143.93        74.47 

$`CD2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
      134.40        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       49.35       133.25        19.04        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL 
      173.85        30.67       144.46        31.76        11.34        42.05 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
      177.86        15.02        22.29        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        24.89         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       75.55        79.20        75.22        76.14        44.28        47.41 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       93.63         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75        23.77        94.19       171.85        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      145.45        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  CD2 MUTATED CD2 WILD-TYPE 
         0.26          0.00 
  CD2 MUTATED CD2 WILD-TYPE 
       227.01        346.49 
  CD2 MUTATED CD2 WILD-TYPE 
       46.720        47.295 
[1] "0.3 - 227.0 (46.7)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.5"
D83V2, survival
               sevent
clus2             0   1
  CD2 MUTATED    14   8
  CD2 WILD-TYPE 110 152
  CD2 MUTATED CD2 WILD-TYPE 
           22           262 
  CD2 MUTATED CD2 WILD-TYPE 
            8           152 
$`CD2 MUTATED`
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A51R TCGA-D3-A5GN 
      126.81        27.35        36.95        90.90        63.81       135.75 
TCGA-D3-A5GO TCGA-D9-A148 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M 
      137.92       151.53        33.73        13.97        63.78        56.84 
TCGA-EE-A29P TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2MF TCGA-EE-A2MJ TCGA-EE-A2MP 
       56.42        75.48        13.91       268.73        96.23       248.65 
TCGA-EE-A2MS TCGA-ER-A19J TCGA-ER-A42L TCGA-GN-A266 
      162.48         6.44       149.03        10.13 

$`CD2 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 
       68.15       168.26         2.60       340.14       134.40        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        26.89       125.79       178.32        18.18       125.19 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        85.08        78.97        72.07        64.64 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
      107.38        54.74        79.66       102.12        42.77        81.21 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT 
      180.39       216.66       167.90        47.54        43.23        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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       152.35 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       33.21        12.95        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        46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  CD2 MUTATED CD2 WILD-TYPE 
         6.44          0.20 
  CD2 MUTATED CD2 WILD-TYPE 
       268.73        369.93 
  CD2 MUTATED CD2 WILD-TYPE 
       69.645        53.175 
[1] "6.4 - 268.7 (69.6)" "0.2 - 369.9 (53.2)"
[1] "hr=" "2"  
D83V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CD2 MUTATED          0       0       3        0        2        5         1
  CD2 WILD-TYPE       10       6      22       10       23       13         9
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CD2 MUTATED           0         2         3          0          2          1
  CD2 WILD-TYPE        14         8        33         14         24         42
               vv
clus            STAGE IV
  CD2 MUTATED          1
  CD2 WILD-TYPE       15
D83V4, multiclass
            clus
vv           CD2 MUTATED CD2 WILD-TYPE
  I/II NOS             0            10
  STAGE 0              0             6
  STAGE I              3            22
  STAGE IA             0            10
  STAGE IB             2            23
  STAGE II             5            13
  STAGE IIA            1             9
  STAGE IIB            0            14
  STAGE IIC            2             8
  STAGE III            3            33
  STAGE IIIA           0            14
  STAGE IIIB           2            24
  STAGE IIIC           1            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
  CD2 MUTATED       1  4  7  5
  CD2 WILD-TYPE    52 58 53 50
D83V5, multiclass
       clus
vv      CD2 MUTATED CD2 WILD-TYPE
  T0+T1           1            52
  T2              4            58
  T3              7            53
  T4              5            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CD2 MUTATED    14   3   2   2
  CD2 WILD-TYPE 129  50  32  33
D83V6, multiclass
    clus
vv   CD2 MUTATED CD2 WILD-TYPE
  N0          14           129
  N1           3            50
  N2           2            32
  N3           2            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"
D83V7, binary
               cls
clus              0   1
  CD2 MUTATED    19   2
  CD2 WILD-TYPE 237  15
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD2 MUTATED     19    2
  CD2 WILD-TYPE  237   15
   clus
vv  CD2 MUTATED CD2 WILD-TYPE
  0          19           237
  1           2            15
[1] 2 2
[1] FALSE
D83V8, binary
               cls
clus             0  1
  CD2 MUTATED    9  4
  CD2 WILD-TYPE 98 69
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD2 MUTATED      9    4
  CD2 WILD-TYPE   98   69
     clus
vv    CD2 MUTATED CD2 WILD-TYPE
  NO            9            98
  YES           4            69
[1] 2 2
[1] FALSE
D83V9, binary
               cls
clus              0   1
  CD2 MUTATED     3  19
  CD2 WILD-TYPE  34 234
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD2 MUTATED      3   19
  CD2 WILD-TYPE   34  234
     clus
vv    CD2 MUTATED CD2 WILD-TYPE
  NO            3            34
  YES          19           234
[1] 2 2
[1] FALSE
D83V10, continuous
D83V11, binary
               cls
clus              0   1
  CD2 MUTATED     8  14
  CD2 WILD-TYPE 101 167
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD2 MUTATED      8   14
  CD2 WILD-TYPE  101  167
        clus
vv       CD2 MUTATED CD2 WILD-TYPE
  FEMALE           8           101
  MALE            14           167
[1] 2 2
[1] FALSE
D83V12, binary
               cls
clus              0   1
  CD2 MUTATED    19   3
  CD2 WILD-TYPE 235  32
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD2 MUTATED     19    3
  CD2 WILD-TYPE  235   32
     clus
vv    CD2 MUTATED CD2 WILD-TYPE
  NO           19           235
  YES           3            32
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD2 MUTATED       0                         0    22
  CD2 WILD-TYPE     5                         1   262
D83V13, multiclass
                           clus
vv                          CD2 MUTATED CD2 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              22           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"
D83V14, binary
               cls
clus              0   1
  CD2 MUTATED     0  22
  CD2 WILD-TYPE   3 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD2 MUTATED      0   22
  CD2 WILD-TYPE    3  261
                        clus
vv                       CD2 MUTATED CD2 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          22           261
[1] 2 2
[1] FALSE

Clustering(84) Variable = CD209 MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2               0   1
  CD209 MUTATED     4   3
  CD209 WILD-TYPE  93 100
  CD209 MUTATED CD209 WILD-TYPE 
              7             193 
  CD209 MUTATED CD209 WILD-TYPE 
              3             100 
$`CD209 MUTATED`
TCGA-EE-A2GD TCGA-FW-A3R5 TCGA-D3-A2JA TCGA-D3-A51T TCGA-D9-A3Z1 TCGA-EB-A5UN 
      269.03        36.85        15.75        11.34        15.02        52.41 
TCGA-EE-A3AF 
        6.28 

$`CD209 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       166.75        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
      134.40        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       25.64        45.99        62.86       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       42.05        45.70       177.86        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       16.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  CD209 MUTATED CD209 WILD-TYPE 
           6.28            0.00 
  CD209 MUTATED CD209 WILD-TYPE 
         269.03          346.49 
  CD209 MUTATED CD209 WILD-TYPE 
          15.75           47.74 
[1] "6.3 - 269.0 (15.8)" "0.0 - 346.5 (47.7)"
[1] "hr=" "1.1"
D84V2, survival
                 sevent
clus2               0   1
  CD209 MUTATED     5   5
  CD209 WILD-TYPE 119 155
  CD209 MUTATED CD209 WILD-TYPE 
             10             274 
  CD209 MUTATED CD209 WILD-TYPE 
              5             155 
$`CD209 MUTATED`
TCGA-EE-A29L TCGA-EE-A2GD TCGA-FW-A3R5 TCGA-D3-A2JA TCGA-D3-A51T TCGA-D9-A3Z1 
        2.60       340.14        36.95       115.53        26.89        15.39 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A3AF TCGA-FS-A1ZA 
       29.29        58.92        13.81        27.72 

$`CD209 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
       68.15       168.26       126.81       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81       125.79       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         7.10 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       20.35         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       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-A3AG 
      124.31       122.73        64.04        28.77        54.51        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  CD209 MUTATED CD209 WILD-TYPE 
            2.6             0.2 
  CD209 MUTATED CD209 WILD-TYPE 
         340.14          369.93 
  CD209 MUTATED CD209 WILD-TYPE 
         28.505          54.460 
[1] "2.6 - 340.1 (28.5)" "0.2 - 369.9 (54.5)"
[1] "hr=" "1"  
D84V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CD209 MUTATED          1       0       0        0        0        0         0
  CD209 WILD-TYPE        9       6      25       10       25       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CD209 MUTATED           1         1         2          1          1
  CD209 WILD-TYPE        13         9        34         13         25
                 vv
clus              STAGE IIIC STAGE IV
  CD209 MUTATED            4        1
  CD209 WILD-TYPE         39       15
D84V4, multiclass
            clus
vv           CD209 MUTATED CD209 WILD-TYPE
  I/II NOS               1               9
  STAGE 0                0               6
  STAGE I                0              25
  STAGE IA               0              10
  STAGE IB               0              25
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              1              13
  STAGE IIC              1               9
  STAGE III              2              34
  STAGE IIIA             1              13
  STAGE IIIB             1              25
  STAGE IIIC             4              39
  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
  CD209 MUTATED       1  3  0  5
  CD209 WILD-TYPE    52 59 60 50
D84V5, multiclass
       clus
vv      CD209 MUTATED CD209 WILD-TYPE
  T0+T1             1              52
  T2                3              59
  T3                0              60
  T4                5              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CD209 MUTATED     2   3   2   3
  CD209 WILD-TYPE 141  50  32  32
D84V6, multiclass
    clus
vv   CD209 MUTATED CD209 WILD-TYPE
  N0             2             141
  N1             3              50
  N2             2              32
  N3             3              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"
D84V7, binary
                 cls
clus                0   1
  CD209 MUTATED    11   1
  CD209 WILD-TYPE 245  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED     11    1
  CD209 WILD-TYPE  245   16
   clus
vv  CD209 MUTATED CD209 WILD-TYPE
  0            11             245
  1             1              16
[1] 2 2
[1] FALSE
D84V8, binary
                 cls
clus                0   1
  CD209 MUTATED     1   5
  CD209 WILD-TYPE 106  68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      1    5
  CD209 WILD-TYPE  106   68
     clus
vv    CD209 MUTATED CD209 WILD-TYPE
  NO              1             106
  YES             5              68
[1] 2 2
[1] FALSE
D84V9, binary
                 cls
clus                0   1
  CD209 MUTATED     1  11
  CD209 WILD-TYPE  36 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      1   11
  CD209 WILD-TYPE   36  242
     clus
vv    CD209 MUTATED CD209 WILD-TYPE
  NO              1              36
  YES            11             242
[1] 2 2
[1] FALSE
D84V10, continuous
D84V11, binary
                 cls
clus                0   1
  CD209 MUTATED     5   7
  CD209 WILD-TYPE 104 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      5    7
  CD209 WILD-TYPE  104  174
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  FEMALE             5             104
  MALE               7             174
[1] 2 2
[1] FALSE
D84V12, binary
                 cls
clus                0   1
  CD209 MUTATED    10   2
  CD209 WILD-TYPE 244  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED     10    2
  CD209 WILD-TYPE  244   33
     clus
vv    CD209 MUTATED CD209 WILD-TYPE
  NO             10             244
  YES             2              33
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD209 MUTATED       0                         0    12
  CD209 WILD-TYPE     5                         1   272
D84V13, multiclass
                           clus
vv                          CD209 MUTATED CD209 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                12             272
[1] 3 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
  CD209 MUTATED     0  12
  CD209 WILD-TYPE   3 271
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      0   12
  CD209 WILD-TYPE    3  271
                        clus
vv                       CD209 MUTATED CD209 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            12             271
[1] 2 2
[1] FALSE

Clustering(85) Variable = C2ORF16 MUTATION ANALYSIS
D85V1, survival
                   sevent
clus2                0  1
  C2ORF16 MUTATED   11  7
  C2ORF16 WILD-TYPE 86 96
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
               18               182 
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
                7                96 
$`C2ORF16 MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JL TCGA-D3-A3MR TCGA-D3-A51R 
      134.40        27.35        36.85       171.58        90.21        62.70 
TCGA-D9-A6EC TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A2GJ TCGA-EE-A2MJ TCGA-EE-A2MS 
       69.21        75.55        12.99        68.65        63.25       143.93 
TCGA-EE-A3AC TCGA-ER-A19D TCGA-ER-A19P TCGA-ER-A42L TCGA-GN-A262 TCGA-RP-A693 
       64.04        11.47       120.76        74.47        53.29         0.33 

$`C2ORF16 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.90        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
       36.30        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        59.70        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       30.67       144.46        31.76        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        15.02        22.29        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
       30.02        77.98        26.14        12.95       201.60        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       94.19       171.85        89.26       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       124.31       122.73         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       53.29        39.81       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       15.48        32.05         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90        18.25         1.91       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 
        7.23         0.20 

  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
             0.33              0.00 
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
           171.58            346.49 
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
           66.345            45.800 
[1] "0.3 - 171.6 (66.3)" "0.0 - 346.5 (45.8)"
[1] "hr=" "1.4"
D85V2, survival
                   sevent
clus2                 0   1
  C2ORF16 MUTATED    15  14
  C2ORF16 WILD-TYPE 109 146
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
               29               255 
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
               14               146 
$`C2ORF16 MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JL TCGA-D3-A3MR TCGA-D3-A51R 
      134.40        27.35        36.95       171.58       103.59        63.81 
TCGA-D9-A1JW TCGA-D9-A6EC TCGA-EB-A5UL TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29N 
        3.65        77.56        29.29       151.27        13.97        18.61 
TCGA-EE-A2GJ TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AC 
      107.38        47.28        96.23        47.54       162.48        64.04 
TCGA-EE-A3AG TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A42L 
       41.59        53.19        12.59        26.37       162.08       149.03 
TCGA-FS-A1ZK TCGA-GF-A6C9 TCGA-GN-A262 TCGA-RP-A693 TCGA-RP-A694 
       23.93        15.78       139.89         0.33         0.69 

$`C2ORF16 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 
       68.15       168.26         2.60       340.14       126.81        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       86.76        11.87       113.52        42.08        12.10        66.48 
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-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        60.23        24.53         9.34        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-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19       151.53        54.67         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
      225.96        43.36        13.87        10.36        20.35        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         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        85.08        78.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        56.42        66.74        14.47        61.28       369.93 
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       115.96        59.64 
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       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       48.72        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       16.96       204.66       180.39       216.66       167.90       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        28.77 
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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        51.35       134.33       152.81 
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-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02       302.07       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 
       44.09        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        93.01        46.98        33.21        12.95        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        46.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      297.90         7.23         0.20 

  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
             0.33              0.20 
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
           171.58            369.93 
  C2ORF16 MUTATED C2ORF16 WILD-TYPE 
            47.54             54.41 
[1] "0.3 - 171.6 (47.5)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1"  
D85V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C2ORF16 MUTATED          2       1       2        1        2        4
  C2ORF16 WILD-TYPE        8       5      23        9       23       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C2ORF16 MUTATED           1         0         0         7          1
  C2ORF16 WILD-TYPE         9        14        10        29         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  C2ORF16 MUTATED            1          1        2
  C2ORF16 WILD-TYPE         25         42       14
D85V4, multiclass
            clus
vv           C2ORF16 MUTATED C2ORF16 WILD-TYPE
  I/II NOS                 2                 8
  STAGE 0                  1                 5
  STAGE I                  2                23
  STAGE IA                 1                 9
  STAGE IB                 2                23
  STAGE II                 4                14
  STAGE IIA                1                 9
  STAGE IIB                0                14
  STAGE IIC                0                10
  STAGE III                7                29
  STAGE IIIA               1                13
  STAGE IIIB               1                25
  STAGE IIIC               1                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
  C2ORF16 MUTATED       5  4  6  2
  C2ORF16 WILD-TYPE    48 58 54 53
D85V5, multiclass
       clus
vv      C2ORF16 MUTATED C2ORF16 WILD-TYPE
  T0+T1               5                48
  T2                  4                58
  T3                  6                54
  T4                  2                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C2ORF16 MUTATED    16   4   5   0
  C2ORF16 WILD-TYPE 127  49  29  35
D85V6, multiclass
    clus
vv   C2ORF16 MUTATED C2ORF16 WILD-TYPE
  N0              16               127
  N1               4                49
  N2               5                29
  N3               0                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"
D85V7, binary
                   cls
clus                  0   1
  C2ORF16 MUTATED    25   2
  C2ORF16 WILD-TYPE 231  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF16 MUTATED     25    2
  C2ORF16 WILD-TYPE  231   15
   clus
vv  C2ORF16 MUTATED C2ORF16 WILD-TYPE
  0              25               231
  1               2                15
[1] 2 2
[1] FALSE
D85V8, binary
                   cls
clus                 0  1
  C2ORF16 MUTATED   11  2
  C2ORF16 WILD-TYPE 96 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF16 MUTATED     11    2
  C2ORF16 WILD-TYPE   96   71
     clus
vv    C2ORF16 MUTATED C2ORF16 WILD-TYPE
  NO               11                96
  YES               2                71
[1] 2 2
[1] FALSE
D85V9, binary
                   cls
clus                  0   1
  C2ORF16 MUTATED     7  22
  C2ORF16 WILD-TYPE  30 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF16 MUTATED      7   22
  C2ORF16 WILD-TYPE   30  231
     clus
vv    C2ORF16 MUTATED C2ORF16 WILD-TYPE
  NO                7                30
  YES              22               231
[1] 2 2
[1] FALSE
D85V10, continuous
D85V11, binary
                   cls
clus                  0   1
  C2ORF16 MUTATED     4  25
  C2ORF16 WILD-TYPE 105 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF16 MUTATED      4   25
  C2ORF16 WILD-TYPE  105  156
        clus
vv       C2ORF16 MUTATED C2ORF16 WILD-TYPE
  FEMALE               4               105
  MALE                25               156
[1] 2 2
[1] FALSE
D85V12, binary
                   cls
clus                  0   1
  C2ORF16 MUTATED    27   2
  C2ORF16 WILD-TYPE 227  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF16 MUTATED     27    2
  C2ORF16 WILD-TYPE  227   33
     clus
vv    C2ORF16 MUTATED C2ORF16 WILD-TYPE
  NO               27               227
  YES               2                33
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C2ORF16 MUTATED       0                         0    29
  C2ORF16 WILD-TYPE     5                         1   255
D85V13, multiclass
                           clus
vv                          C2ORF16 MUTATED C2ORF16 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  29               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"
D85V14, binary
                   cls
clus                  0   1
  C2ORF16 MUTATED     0  29
  C2ORF16 WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF16 MUTATED      0   29
  C2ORF16 WILD-TYPE    3  254
                        clus
vv                       C2ORF16 MUTATED C2ORF16 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              29               254
[1] 2 2
[1] FALSE

Clustering(86) Variable = GLRB MUTATION ANALYSIS
D86V1, survival
                sevent
clus2             0  1
  GLRB MUTATED    9 14
  GLRB WILD-TYPE 88 89
  GLRB MUTATED GLRB WILD-TYPE 
            23            177 
  GLRB MUTATED GLRB WILD-TYPE 
            14             89 
$`GLRB MUTATED`
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2J8 
       62.07       166.75       269.03        27.35        36.85        62.86 
TCGA-D9-A6EC TCGA-EE-A182 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GP TCGA-EE-A2MF 
       69.21         0.00        12.99         0.26         0.76       209.79 
TCGA-EE-A2MS TCGA-EE-A3AE TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A42L TCGA-FS-A1YW 
      143.93        54.51         4.54        11.47        74.47       171.78 
TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-GN-A4U4 
       43.92       130.95         4.47         3.06        34.49 

$`GLRB WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
       38.76        33.24        31.96        52.90       134.40        19.04 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        8.42        15.72        31.89       110.93        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA 
       19.04        76.41        62.60        25.64        45.99        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
      177.86        15.02        22.29        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20C 
       18.21        13.15        24.89        20.38        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       79.20        75.22        76.14        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       32.48        18.35        93.63         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
      103.13        15.25         5.75        23.77        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       227.01        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        64.04         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       67.89       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      135.98        34.45        10.49         7.82        53.29        39.81 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       32.05         4.50       174.21        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       27.62       312.07        32.78         7.82        36.33        78.61 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
      136.27        35.28        23.21         5.29        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-OD-A75X 
       17.06        42.48         7.59       120.53        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  GLRB MUTATED GLRB WILD-TYPE 
           0.0            0.2 
  GLRB MUTATED GLRB WILD-TYPE 
        269.03         346.49 
  GLRB MUTATED GLRB WILD-TYPE 
         43.92          47.41 
[1] "0.0 - 269.0 (43.9)" "0.2 - 346.5 (47.4)"
[1] "hr=" "1.2"
D86V2, survival
                sevent
clus2              0   1
  GLRB MUTATED    12  18
  GLRB WILD-TYPE 112 142
  GLRB MUTATED GLRB WILD-TYPE 
            30            254 
  GLRB MUTATED GLRB WILD-TYPE 
            18            142 
$`GLRB MUTATED`
TCGA-D3-A2JF TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A3JD TCGA-FW-A3R5 
       62.07       168.26         2.60       340.14        27.35        36.95 
TCGA-D3-A2J8 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-EE-A182 TCGA-EE-A29D TCGA-EE-A29E 
       65.49        25.18        77.56        14.70        13.97        63.78 
TCGA-EE-A2GC TCGA-EE-A2GP TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MS TCGA-EE-A3AE 
       67.43        13.91        47.28       268.73       162.48        54.51 
TCGA-EE-A3J5 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A42L TCGA-FS-A1YW TCGA-FS-A1ZE 
       36.95        77.75        12.59       149.03       216.92        46.45 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-GF-A6C9 TCGA-GN-A4U4 
       74.73       133.55        26.56        27.02        15.78        39.35 

$`GLRB WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 
      126.81       134.40        31.40        50.76        15.45        16.57 
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-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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       63.35        85.08        78.97        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
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       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.29        86.14        59.28       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
      107.38        54.74        79.66        75.48       102.12        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        61.51       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        13.81        41.59       138.81       172.18       127.20 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      152.81        35.44        13.94         9.17        98.40        48.89 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1YY 
       12.95        92.98       174.21        15.72        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        53.52         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26        11.41       148.80        53.16        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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        19.43         2.04       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  GLRB MUTATED GLRB WILD-TYPE 
           2.6            0.2 
  GLRB MUTATED GLRB WILD-TYPE 
        340.14         369.93 
  GLRB MUTATED GLRB WILD-TYPE 
        50.895         53.970 
[1] "2.6 - 340.1 (50.9)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1"  
D86V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  GLRB MUTATED          1       0       2        2        3        4         1
  GLRB WILD-TYPE        9       6      23        8       22       14         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GLRB MUTATED           3         2         3          1          3          4
  GLRB WILD-TYPE        11         8        33         13         23         39
                vv
clus             STAGE IV
  GLRB MUTATED          1
  GLRB WILD-TYPE       15
D86V4, multiclass
            clus
vv           GLRB MUTATED GLRB WILD-TYPE
  I/II NOS              1              9
  STAGE 0               0              6
  STAGE I               2             23
  STAGE IA              2              8
  STAGE IB              3             22
  STAGE II              4             14
  STAGE IIA             1              9
  STAGE IIB             3             11
  STAGE IIC             2              8
  STAGE III             3             33
  STAGE IIIA            1             13
  STAGE IIIB            3             23
  STAGE IIIC            4             39
  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
  GLRB MUTATED       3  5  9  8
  GLRB WILD-TYPE    50 57 51 47
D86V5, multiclass
       clus
vv      GLRB MUTATED GLRB WILD-TYPE
  T0+T1            3             50
  T2               5             57
  T3               9             51
  T4               8             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GLRB MUTATED    18   6   2   2
  GLRB WILD-TYPE 125  47  32  33
D86V6, multiclass
    clus
vv   GLRB MUTATED GLRB WILD-TYPE
  N0           18            125
  N1            6             47
  N2            2             32
  N3            2             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"
D86V7, binary
                cls
clus               0   1
  GLRB MUTATED    28   1
  GLRB WILD-TYPE 228  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED     28    1
  GLRB WILD-TYPE  228   16
   clus
vv  GLRB MUTATED GLRB WILD-TYPE
  0           28            228
  1            1             16
[1] 2 2
[1] FALSE
D86V8, binary
                cls
clus              0  1
  GLRB MUTATED   11 11
  GLRB WILD-TYPE 96 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED     11   11
  GLRB WILD-TYPE   96   62
     clus
vv    GLRB MUTATED GLRB WILD-TYPE
  NO            11             96
  YES           11             62
[1] 2 2
[1] FALSE
D86V9, binary
                cls
clus               0   1
  GLRB MUTATED     3  27
  GLRB WILD-TYPE  34 226
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED      3   27
  GLRB WILD-TYPE   34  226
     clus
vv    GLRB MUTATED GLRB WILD-TYPE
  NO             3             34
  YES           27            226
[1] 2 2
[1] FALSE
D86V10, continuous
D86V11, binary
                cls
clus               0   1
  GLRB MUTATED     7  23
  GLRB WILD-TYPE 102 158
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED      7   23
  GLRB WILD-TYPE  102  158
        clus
vv       GLRB MUTATED GLRB WILD-TYPE
  FEMALE            7            102
  MALE             23            158
[1] 2 2
[1] FALSE
D86V12, binary
                cls
clus               0   1
  GLRB MUTATED    27   3
  GLRB WILD-TYPE 227  32
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED     27    3
  GLRB WILD-TYPE  227   32
     clus
vv    GLRB MUTATED GLRB WILD-TYPE
  NO            27            227
  YES            3             32
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GLRB MUTATED       0                         0    30
  GLRB WILD-TYPE     5                         1   254
D86V13, multiclass
                           clus
vv                          GLRB MUTATED GLRB WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               30            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"
D86V14, binary
                cls
clus               0   1
  GLRB MUTATED     1  29
  GLRB WILD-TYPE   2 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED      1   29
  GLRB WILD-TYPE    2  254
                        clus
vv                       GLRB MUTATED GLRB WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           29            254
[1] 2 2
[1] FALSE

Clustering(87) Variable = PKDREJ MUTATION ANALYSIS
D87V1, survival
                  sevent
clus2               0  1
  PKDREJ MUTATED   11 11
  PKDREJ WILD-TYPE 86 92
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              22              178 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              11               92 
$`PKDREJ MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-D3-A2J7 
       52.90       134.40        27.35        36.85       110.93        45.99 
TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA 
       20.38        75.55         0.26       227.01       143.93       124.31 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3TU 
       99.06        59.84       120.76         4.47        23.21        55.59 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A268 TCGA-QB-A6FS 
       18.25        96.92        42.48         7.23 

$`PKDREJ WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       19.04         8.42        15.72        31.89        49.35       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        76.41        62.60        25.64        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
      177.86        15.02        22.29        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
       52.41        18.21        13.15        24.89         0.00        26.24 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14        12.99        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      145.45        23.51        53.26       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.51        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       43.92         7.82        36.33        78.61       130.95       136.27 
TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       35.28         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       13.28        80.68        11.54        19.30         9.90         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       53.29       117.93        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         0.20         0.33 

  PKDREJ MUTATED PKDREJ WILD-TYPE 
            0.26             0.00 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
          227.01           346.49 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
          54.245           47.050 
[1] "0.3 - 227.0 (54.2)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1"  
D87V2, survival
                  sevent
clus2                0   1
  PKDREJ MUTATED    13  17
  PKDREJ WILD-TYPE 111 143
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              30              254 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              17              143 
$`PKDREJ MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-D3-A2J7 
      126.81       134.40        27.35        36.95       112.57       103.10 
TCGA-D3-A5GU TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A2GI 
      125.19        33.73         4.96       151.27        63.78        48.72 
TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AG TCGA-EE-A3J5 
       21.67       248.65       162.48       124.31        41.59        36.95 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A42K TCGA-FS-A1ZU TCGA-FS-A1ZW 
      131.51        61.05       162.08        12.95        26.56        49.48 
TCGA-FS-A4FC TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A268 TCGA-QB-A6FS 
       54.41        55.59        19.43        96.92        62.79         7.23 

$`PKDREJ WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-ER-A193 TCGA-ER-A198 
       68.15       168.26         2.60       340.14        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       15.45        16.57        16.67       112.04        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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I 
        8.65        14.70        26.89       133.81        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        13.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        42.77        81.21        44.88        94.82       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       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      167.90        47.54        43.23        71.21        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       64.04        28.77        54.51        13.81       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-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      152.35         6.44        44.09        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        46.45         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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      148.80        53.16        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73       174.84        34.03        26.73        80.68        17.46 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       13.51        19.30         9.90         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
      117.93        10.13        64.44        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 
       39.35        10.42        48.89        22.13       297.90         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  PKDREJ MUTATED PKDREJ WILD-TYPE 
            4.96             0.20 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
          248.65           369.93 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
           58.32            53.39 
[1] "5.0 - 248.7 (58.3)" "0.2 - 369.9 (53.4)"
[1] "hr=" "1"  
D87V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  PKDREJ MUTATED          1       1       3        1        2        3
  PKDREJ WILD-TYPE        9       5      22        9       23       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  PKDREJ MUTATED           1         1         1         5          0
  PKDREJ WILD-TYPE         9        13         9        31         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  PKDREJ MUTATED            2          5        0
  PKDREJ WILD-TYPE         24         38       16
D87V4, multiclass
            clus
vv           PKDREJ MUTATED PKDREJ WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 1                5
  STAGE I                 3               22
  STAGE IA                1                9
  STAGE IB                2               23
  STAGE II                3               15
  STAGE IIA               1                9
  STAGE IIB               1               13
  STAGE IIC               1                9
  STAGE III               5               31
  STAGE IIIA              0               14
  STAGE IIIB              2               24
  STAGE IIIC              5               38
  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
  PKDREJ MUTATED       6  5  6  5
  PKDREJ WILD-TYPE    47 57 54 50
D87V5, multiclass
       clus
vv      PKDREJ MUTATED PKDREJ WILD-TYPE
  T0+T1              6               47
  T2                 5               57
  T3                 6               54
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PKDREJ MUTATED    15   4   4   4
  PKDREJ WILD-TYPE 128  49  30  31
D87V6, multiclass
    clus
vv   PKDREJ MUTATED PKDREJ WILD-TYPE
  N0             15              128
  N1              4               49
  N2              4               30
  N3              4               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"
D87V7, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    27   0
  PKDREJ WILD-TYPE 229  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     27    0
  PKDREJ WILD-TYPE  229   17
   clus
vv  PKDREJ MUTATED PKDREJ WILD-TYPE
  0             27              229
  1              0               17
[1] 2 2
[1] FALSE
D87V8, binary
                  cls
clus                0  1
  PKDREJ MUTATED   11  5
  PKDREJ WILD-TYPE 96 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     11    5
  PKDREJ WILD-TYPE   96   68
     clus
vv    PKDREJ MUTATED PKDREJ WILD-TYPE
  NO              11               96
  YES              5               68
[1] 2 2
[1] FALSE
D87V9, binary
                  cls
clus                 0   1
  PKDREJ MUTATED     6  24
  PKDREJ WILD-TYPE  31 229
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED      6   24
  PKDREJ WILD-TYPE   31  229
     clus
vv    PKDREJ MUTATED PKDREJ WILD-TYPE
  NO               6               31
  YES             24              229
[1] 2 2
[1] FALSE
D87V10, continuous
D87V11, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    11  19
  PKDREJ WILD-TYPE  98 162
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     11   19
  PKDREJ WILD-TYPE   98  162
        clus
vv       PKDREJ MUTATED PKDREJ WILD-TYPE
  FEMALE             11               98
  MALE               19              162
[1] 2 2
[1] FALSE
D87V12, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    28   2
  PKDREJ WILD-TYPE 226  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     28    2
  PKDREJ WILD-TYPE  226   33
     clus
vv    PKDREJ MUTATED PKDREJ WILD-TYPE
  NO              28              226
  YES              2               33
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PKDREJ MUTATED       0                         0    30
  PKDREJ WILD-TYPE     5                         1   254
D87V13, multiclass
                           clus
vv                          PKDREJ MUTATED PKDREJ WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 30              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"
D87V14, binary
                  cls
clus                 0   1
  PKDREJ MUTATED     0  30
  PKDREJ WILD-TYPE   3 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED      0   30
  PKDREJ WILD-TYPE    3  253
                        clus
vv                       PKDREJ MUTATED PKDREJ WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             30              253
[1] 2 2
[1] FALSE

Clustering(88) Variable = PTPRT MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2              0  1
  PTPRT MUTATED   39 21
  PTPRT WILD-TYPE 58 82
  PTPRT MUTATED PTPRT WILD-TYPE 
             60             140 
  PTPRT MUTATED PTPRT WILD-TYPE 
             21              82 
$`PTPRT MUTATED`
TCGA-D3-A2JF TCGA-EE-A180 TCGA-EE-A2MR TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q6 
       62.07        31.96       134.40        27.35        36.85        49.35 
TCGA-D3-A1QA TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       76.41        36.30        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GL TCGA-D9-A6EC 
      140.98        90.21       173.85        11.34        42.05        69.21 
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A181 
       76.34        68.68       110.53        42.64        52.41        20.38 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
       26.24        75.55        12.99         0.26        47.41        27.16 
TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GR 
      346.49       115.43        26.14       201.60        18.35         0.20 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MM 
       71.31       103.13       209.79       171.85        63.25       145.45 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-ER-A19G TCGA-ER-A2NE 
      143.93        53.26       124.31        64.04       184.60        16.87 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FS-A1ZD TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ 
       32.05        74.47        32.78       130.95       136.27         3.06 
TCGA-FS-A4F0 TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-OD-A75X TCGA-RP-A693 
       18.51         1.91        53.29       117.93       297.01         0.33 

$`PTPRT WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A193 
       38.76        33.24       166.75       269.03        52.90        19.04 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.42        15.72        31.89       110.93       133.25        19.04 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       86.30       107.61       171.58        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        9.34        23.67        30.67       144.46        31.76        62.70 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY 
       45.70       177.86        15.02        22.29        22.85       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61        60.10        64.83        58.85        30.44       225.11 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
        3.91        16.41        18.21        13.15        24.89         0.00 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29Q 
       79.20        75.22        76.14        44.28        47.74        61.12 
TCGA-EE-A29W TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
      185.19        30.02        77.98        12.95        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
       32.48        93.63         0.76        81.99        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MT 
       23.77        94.19        89.26       104.78       227.01        23.51 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       47.18       146.63        73.05        22.36         4.70        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       28.67       173.29        68.52        15.48         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU 
       43.92         7.82        36.33        78.61        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
       23.21         5.29        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 
       55.59        11.54        19.30         9.90        18.25        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-QB-A6FS TCGA-RP-A690 
        7.23         0.20 

  PTPRT MUTATED PTPRT WILD-TYPE 
            0.2             0.0 
  PTPRT MUTATED PTPRT WILD-TYPE 
         346.49          312.07 
  PTPRT MUTATED PTPRT WILD-TYPE 
         62.660          43.215 
[1] "0.2 - 346.5 (62.7)" "0.0 - 312.1 (43.2)"
[1] "hr=" "2.1"
D88V2, survival
                 sevent
clus2               0   1
  PTPRT MUTATED    47  36
  PTPRT WILD-TYPE  77 124
  PTPRT MUTATED PTPRT WILD-TYPE 
             83             201 
  PTPRT MUTATED PTPRT WILD-TYPE 
             36             124 
$`PTPRT MUTATED`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A2MR TCGA-EE-A3JD 
       62.07        13.87        94.98        68.15       134.40        27.35 
TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JO 
       36.95        71.80        90.90        42.08        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A51E 
       59.57        58.06        46.98       166.52       103.59       174.84 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
       26.89       125.79        25.18        77.56        76.57       222.51 
TCGA-DA-A1I5 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A183 
      135.02        10.49        43.36        58.92        33.73        26.89 
TCGA-EE-A20C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29R 
      151.27        13.97        63.78        64.64        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GH 
      369.93        25.87       115.96        59.28        67.43       220.24 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       48.72        75.48        42.77        81.21        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-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AH 
       43.23       162.48        53.26       124.31        64.04       138.81 
TCGA-EE-A3JA TCGA-ER-A19G TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3PL TCGA-ER-A42L 
       53.19       302.07        20.15        41.56        33.21       149.03 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        7.79        27.72        53.52        23.93       133.55       148.80 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       27.02        77.82        54.41         2.04       139.89       117.93 
TCGA-GN-A266 TCGA-GN-A4U7 TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 
       10.13        10.42       297.90         0.33         0.69 

$`PTPRT WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD 
       46.32        68.25        54.02       168.26         2.60       340.14 
TCGA-EE-A2GO TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 
      126.81        31.40        50.76        15.45        16.57        16.67 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
      112.04       112.57       133.25        28.08        31.59        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ 
       86.76        11.87       113.52        12.10       171.58       130.72 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       86.93        60.23        24.53         9.34        39.75        45.30 
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-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         7.10        15.39        22.29         9.90 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        36.03       144.89        20.38       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV 
      225.96        13.87        10.36        20.35        29.29         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 
       36.46        29.82        27.22         8.65        14.70         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W 
       72.07        56.84        18.61        66.74        61.28       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE 
       17.92        46.82        59.64        39.29        86.14       173.79 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU 
      107.38        54.74        79.66       102.12        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 
      180.39       216.66        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 
       28.77        54.51        13.81        41.59       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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        13.02        26.37       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
        8.88       148.18       105.07        43.82        23.34        28.83 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       48.99       247.04        93.01        46.98        12.95        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-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZG 
       20.91        28.08        48.85       357.37        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT 
       32.75        47.38       101.26        74.73        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        49.48        27.09        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A267 
       19.30         9.90        19.43        15.78        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       62.79        32.48        48.00       121.91        39.35        48.89 
TCGA-GN-A4U9 TCGA-QB-A6FS TCGA-RP-A690 
       22.13         7.23         0.20 

  PTPRT MUTATED PTPRT WILD-TYPE 
           0.33            0.20 
  PTPRT MUTATED PTPRT WILD-TYPE 
         369.93          357.37 
  PTPRT MUTATED PTPRT WILD-TYPE 
          62.07           49.48 
[1] "0.3 - 369.9 (62.1)" "0.2 - 357.4 (49.5)"
[1] "hr=" "1.7"
D88V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PTPRT MUTATED          5       3       7        4        8        7         3
  PTPRT WILD-TYPE        5       3      18        6       17       11         7
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PTPRT MUTATED           5         3        11          3          6
  PTPRT WILD-TYPE         9         7        25         11         20
                 vv
clus              STAGE IIIC STAGE IV
  PTPRT MUTATED           10        5
  PTPRT WILD-TYPE         33       11
D88V4, multiclass
            clus
vv           PTPRT MUTATED PTPRT WILD-TYPE
  I/II NOS               5               5
  STAGE 0                3               3
  STAGE I                7              18
  STAGE IA               4               6
  STAGE IB               8              17
  STAGE II               7              11
  STAGE IIA              3               7
  STAGE IIB              5               9
  STAGE IIC              3               7
  STAGE III             11              25
  STAGE IIIA             3              11
  STAGE IIIB             6              20
  STAGE IIIC            10              33
  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 19 19 14
  PTPRT WILD-TYPE    37 43 41 41
D88V5, multiclass
       clus
vv      PTPRT MUTATED PTPRT WILD-TYPE
  T0+T1            16              37
  T2               19              43
  T3               19              41
  T4               14              41
[1] 4 2
[1] TRUE
[1] "dimension of 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   48 12 11  5
  PTPRT WILD-TYPE 95 41 23 30
D88V6, multiclass
    clus
vv   PTPRT MUTATED PTPRT WILD-TYPE
  N0            48              95
  N1            12              41
  N2            11              23
  N3             5              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"
D88V7, binary
                 cls
clus                0   1
  PTPRT MUTATED    78   5
  PTPRT WILD-TYPE 178  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     78    5
  PTPRT WILD-TYPE  178   12
   clus
vv  PTPRT MUTATED PTPRT WILD-TYPE
  0            78             178
  1             5              12
[1] 2 2
[1] FALSE
D88V8, binary
                 cls
clus               0  1
  PTPRT MUTATED   34 17
  PTPRT WILD-TYPE 73 56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     34   17
  PTPRT WILD-TYPE   73   56
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             34              73
  YES            17              56
[1] 2 2
[1] FALSE
D88V9, binary
                 cls
clus                0   1
  PTPRT MUTATED    13  73
  PTPRT WILD-TYPE  24 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     13   73
  PTPRT WILD-TYPE   24  180
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             13              24
  YES            73             180
[1] 2 2
[1] FALSE
D88V10, continuous
D88V11, binary
                 cls
clus                0   1
  PTPRT MUTATED    27  59
  PTPRT WILD-TYPE  82 122
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     27   59
  PTPRT WILD-TYPE   82  122
        clus
vv       PTPRT MUTATED PTPRT WILD-TYPE
  FEMALE            27              82
  MALE              59             122
[1] 2 2
[1] FALSE
D88V12, binary
                 cls
clus                0   1
  PTPRT MUTATED    75  11
  PTPRT WILD-TYPE 179  24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     75   11
  PTPRT WILD-TYPE  179   24
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             75             179
  YES            11              24
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPRT MUTATED       0                         0    86
  PTPRT WILD-TYPE     5                         1   198
D88V13, multiclass
                           clus
vv                          PTPRT MUTATED PTPRT WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                86             198
[1] 3 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
  PTPRT MUTATED     1  85
  PTPRT WILD-TYPE   2 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED      1   85
  PTPRT WILD-TYPE    2  198
                        clus
vv                       PTPRT MUTATED PTPRT WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            85             198
[1] 2 2
[1] FALSE

Clustering(89) Variable = FAM55C MUTATION ANALYSIS
D89V1, survival
                  sevent
clus2               0  1
  FAM55C MUTATED    1  5
  FAM55C WILD-TYPE 96 98
  FAM55C MUTATED FAM55C WILD-TYPE 
               6              194 
  FAM55C MUTATED FAM55C WILD-TYPE 
               5               98 
$`FAM55C MUTATED`
TCGA-FW-A3R5 TCGA-EE-A29D TCGA-EE-A29Q TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-ER-A19M 
       36.85        12.99        61.12         0.76        63.25        59.84 

$`FAM55C WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        27.35        19.04         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        47.74        27.16       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       10.62        32.48        18.35        93.63         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       94.19       171.85        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  FAM55C MUTATED FAM55C WILD-TYPE 
            0.76             0.00 
  FAM55C MUTATED FAM55C WILD-TYPE 
           63.25           346.49 
  FAM55C MUTATED FAM55C WILD-TYPE 
          48.345           47.295 
[1] "0.8 - 63.2 (48.3)"  "0.0 - 346.5 (47.3)"
[1] "hr=" "2.9"
D89V2, survival
                  sevent
clus2                0   1
  FAM55C MUTATED     1   5
  FAM55C WILD-TYPE 123 155
  FAM55C MUTATED FAM55C WILD-TYPE 
               6              278 
  FAM55C MUTATED FAM55C WILD-TYPE 
               5              155 
$`FAM55C MUTATED`
TCGA-FW-A3R5 TCGA-EE-A29D TCGA-EE-A29Q TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-ER-A19M 
       36.95        13.97        66.74        13.91        96.23        61.05 

$`FAM55C WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       27.35        31.40        50.76        15.45        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12        42.77        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         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        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  FAM55C MUTATED FAM55C WILD-TYPE 
           13.91             0.20 
  FAM55C MUTATED FAM55C WILD-TYPE 
           96.23           369.93 
  FAM55C MUTATED FAM55C WILD-TYPE 
           49.00            53.97 
[1] "13.9 - 96.2 (49.0)" "0.2 - 369.9 (54.0)"
[1] "hr=" "2.2"
D89V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  FAM55C MUTATED          0       0       0        0        1        0
  FAM55C WILD-TYPE       10       6      25       10       24       18
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  FAM55C MUTATED           0         1         0         2          0
  FAM55C WILD-TYPE        10        13        10        34         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  FAM55C MUTATED            1          1        0
  FAM55C WILD-TYPE         25         42       16
D89V4, multiclass
            clus
vv           FAM55C MUTATED FAM55C WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 0               25
  STAGE IA                0               10
  STAGE IB                1               24
  STAGE II                0               18
  STAGE IIA               0               10
  STAGE IIB               1               13
  STAGE IIC               0               10
  STAGE III               2               34
  STAGE IIIA              0               14
  STAGE IIIB              1               25
  STAGE IIIC              1               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
  FAM55C MUTATED       0  1  2  2
  FAM55C WILD-TYPE    53 61 58 53
D89V5, multiclass
       clus
vv      FAM55C MUTATED FAM55C WILD-TYPE
  T0+T1              0               53
  T2                 1               61
  T3                 2               58
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM55C MUTATED     3   2   1   0
  FAM55C WILD-TYPE 140  51  33  35
D89V6, multiclass
    clus
vv   FAM55C MUTATED FAM55C WILD-TYPE
  N0              3              140
  N1              2               51
  N2              1               33
  N3              0               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"
D89V7, binary
                  cls
clus                 0   1
  FAM55C MUTATED     6   0
  FAM55C WILD-TYPE 250  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      6    0
  FAM55C WILD-TYPE  250   17
   clus
vv  FAM55C MUTATED FAM55C WILD-TYPE
  0              6              250
  1              0               17
[1] 2 2
[1] FALSE
D89V8, binary
                  cls
clus                 0   1
  FAM55C MUTATED     2   3
  FAM55C WILD-TYPE 105  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      2    3
  FAM55C WILD-TYPE  105   70
     clus
vv    FAM55C MUTATED FAM55C WILD-TYPE
  NO               2              105
  YES              3               70
[1] 2 2
[1] FALSE
D89V9, binary
                  cls
clus                 0   1
  FAM55C MUTATED     0   6
  FAM55C WILD-TYPE  37 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      0    6
  FAM55C WILD-TYPE   37  247
     clus
vv    FAM55C MUTATED FAM55C WILD-TYPE
  NO               0               37
  YES              6              247
[1] 2 2
[1] FALSE
D89V10, continuous
D89V11, binary
                  cls
clus                 0   1
  FAM55C MUTATED     1   5
  FAM55C WILD-TYPE 108 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      1    5
  FAM55C WILD-TYPE  108  176
        clus
vv       FAM55C MUTATED FAM55C WILD-TYPE
  FEMALE              1              108
  MALE                5              176
[1] 2 2
[1] FALSE
D89V12, binary
                  cls
clus                 0   1
  FAM55C MUTATED     6   0
  FAM55C WILD-TYPE 248  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      6    0
  FAM55C WILD-TYPE  248   35
     clus
vv    FAM55C MUTATED FAM55C WILD-TYPE
  NO               6              248
  YES              0               35
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM55C MUTATED       0                         0     6
  FAM55C WILD-TYPE     5                         1   278
D89V13, multiclass
                           clus
vv                          FAM55C MUTATED FAM55C WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  6              278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V14, binary
                  cls
clus                 0   1
  FAM55C MUTATED     0   6
  FAM55C WILD-TYPE   3 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM55C MUTATED      0    6
  FAM55C WILD-TYPE    3  277
                        clus
vv                       FAM55C MUTATED FAM55C WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              6              277
[1] 2 2
[1] FALSE

Clustering(90) Variable = NUDT4 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  NUDT4 MUTATED     2   2
  NUDT4 WILD-TYPE  95 101
  NUDT4 MUTATED NUDT4 WILD-TYPE 
              4             196 
  NUDT4 MUTATED NUDT4 WILD-TYPE 
              2             101 
$`NUDT4 MUTATED`
TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19G 
       75.55         0.26        44.28       184.60 

$`NUDT4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
      177.86        15.02        22.29        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       26.24        79.20        75.22        76.14        12.99        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.47       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  NUDT4 MUTATED NUDT4 WILD-TYPE 
           0.26            0.00 
  NUDT4 MUTATED NUDT4 WILD-TYPE 
         184.60          346.49 
  NUDT4 MUTATED NUDT4 WILD-TYPE 
         59.915          47.295 
[1] "0.3 - 184.6 (59.9)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.2"
D90V2, survival
                 sevent
clus2               0   1
  NUDT4 MUTATED     2   3
  NUDT4 WILD-TYPE 122 157
  NUDT4 MUTATED NUDT4 WILD-TYPE 
              5             279 
  NUDT4 MUTATED NUDT4 WILD-TYPE 
              3             157 
$`NUDT4 MUTATED`
TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19G TCGA-FS-A1ZA 
      151.27        63.78        72.07       302.07        27.72 

$`NUDT4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81        91.56        13.55        63.35        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97        64.64        56.84        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 
       10.13        64.44        62.79        32.48        48.00       121.91 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.35        10.42        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  NUDT4 MUTATED NUDT4 WILD-TYPE 
          27.72            0.20 
  NUDT4 MUTATED NUDT4 WILD-TYPE 
         302.07          369.93 
  NUDT4 MUTATED NUDT4 WILD-TYPE 
          72.07           53.52 
[1] "27.7 - 302.1 (72.1)" "0.2 - 369.9 (53.5)" 
[1] "hr=" "1.6"
D90V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  NUDT4 MUTATED          0       1       0        0        0        0         0
  NUDT4 WILD-TYPE       10       5      25       10       25       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NUDT4 MUTATED           0         0         0          1          2
  NUDT4 WILD-TYPE        14        10        36         13         24
                 vv
clus              STAGE IIIC STAGE IV
  NUDT4 MUTATED            0        0
  NUDT4 WILD-TYPE         43       16
D90V4, multiclass
            clus
vv           NUDT4 MUTATED NUDT4 WILD-TYPE
  I/II NOS               0              10
  STAGE 0                1               5
  STAGE I                0              25
  STAGE IA               0              10
  STAGE IB               0              25
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              0              36
  STAGE IIIA             1              13
  STAGE IIIB             2              24
  STAGE IIIC             0              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
  NUDT4 MUTATED       0  0  1  2
  NUDT4 WILD-TYPE    53 62 59 53
D90V5, multiclass
       clus
vv      NUDT4 MUTATED NUDT4 WILD-TYPE
  T0+T1             0              53
  T2                0              62
  T3                1              59
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NUDT4 MUTATED     2   1   2   0
  NUDT4 WILD-TYPE 141  52  32  35
D90V6, multiclass
    clus
vv   NUDT4 MUTATED NUDT4 WILD-TYPE
  N0             2             141
  N1             1              52
  N2             2              32
  N3             0              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"
D90V7, binary
                 cls
clus                0   1
  NUDT4 MUTATED     5   0
  NUDT4 WILD-TYPE 251  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUDT4 MUTATED      5    0
  NUDT4 WILD-TYPE  251   17
   clus
vv  NUDT4 MUTATED NUDT4 WILD-TYPE
  0             5             251
  1             0              17
[1] 2 2
[1] FALSE
D90V8, binary
                 cls
clus                0   1
  NUDT4 MUTATED     3   1
  NUDT4 WILD-TYPE 104  72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUDT4 MUTATED      3    1
  NUDT4 WILD-TYPE  104   72
     clus
vv    NUDT4 MUTATED NUDT4 WILD-TYPE
  NO              3             104
  YES             1              72
[1] 2 2
[1] FALSE
D90V9, binary
                 cls
clus                0   1
  NUDT4 MUTATED     0   5
  NUDT4 WILD-TYPE  37 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUDT4 MUTATED      0    5
  NUDT4 WILD-TYPE   37  248
     clus
vv    NUDT4 MUTATED NUDT4 WILD-TYPE
  NO              0              37
  YES             5             248
[1] 2 2
[1] FALSE
D90V10, continuous
D90V11, binary
                 cls
clus                0   1
  NUDT4 MUTATED     2   3
  NUDT4 WILD-TYPE 107 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUDT4 MUTATED      2    3
  NUDT4 WILD-TYPE  107  178
        clus
vv       NUDT4 MUTATED NUDT4 WILD-TYPE
  FEMALE             2             107
  MALE               3             178
[1] 2 2
[1] FALSE
D90V12, binary
                 cls
clus                0   1
  NUDT4 MUTATED     5   0
  NUDT4 WILD-TYPE 249  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUDT4 MUTATED      5    0
  NUDT4 WILD-TYPE  249   35
     clus
vv    NUDT4 MUTATED NUDT4 WILD-TYPE
  NO              5             249
  YES             0              35
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUDT4 MUTATED       0                         0     5
  NUDT4 WILD-TYPE     5                         1   279
D90V13, multiclass
                           clus
vv                          NUDT4 MUTATED NUDT4 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 5             279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V14, binary
                 cls
clus                0   1
  NUDT4 MUTATED     0   5
  NUDT4 WILD-TYPE   3 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUDT4 MUTATED      0    5
  NUDT4 WILD-TYPE    3  278
                        clus
vv                       NUDT4 MUTATED NUDT4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5             278
[1] 2 2
[1] FALSE

Clustering(91) Variable = MYPOP MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2              0  1
  MYPOP MUTATED    1  5
  MYPOP WILD-TYPE 96 98
  MYPOP MUTATED MYPOP WILD-TYPE 
              6             194 
  MYPOP MUTATED MYPOP WILD-TYPE 
              5              98 
$`MYPOP MUTATED`
TCGA-D3-A2JG TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2MS 
      107.61       225.11        24.89        20.38        12.99       143.93 

$`MYPOP WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      168.00        86.30        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       30.44        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       13.15         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14         0.26        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.51        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H 
        4.54        53.29        39.81        11.47       184.60       150.12 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  MYPOP MUTATED MYPOP WILD-TYPE 
          12.99            0.00 
  MYPOP MUTATED MYPOP WILD-TYPE 
         225.11          346.49 
  MYPOP MUTATED MYPOP WILD-TYPE 
         66.250          47.295 
[1] "13.0 - 225.1 (66.2)" "0.0 - 346.5 (47.3)" 
[1] "hr=" "1.3"
D91V2, survival
                 sevent
clus2               0   1
  MYPOP MUTATED     2   5
  MYPOP WILD-TYPE 122 155
  MYPOP MUTATED MYPOP WILD-TYPE 
              7             277 
  MYPOP MUTATED MYPOP WILD-TYPE 
              5             155 
$`MYPOP MUTATED`
TCGA-D3-A2JG TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A2GI 
      113.52       225.96        27.22        33.73        13.97        48.72 
TCGA-EE-A2MS 
      162.48 

$`MYPOP WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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-A2JH 
       23.77       115.53       168.00        86.76        11.87        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
       10.49        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       58.92         7.04        36.46        29.82         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        42.77        81.21        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       180.39 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      216.66       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-A3AE 
       53.26       124.31       122.73        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  MYPOP MUTATED MYPOP WILD-TYPE 
          13.97            0.20 
  MYPOP MUTATED MYPOP WILD-TYPE 
         225.96          369.93 
  MYPOP MUTATED MYPOP WILD-TYPE 
          48.72           54.02 
[1] "14.0 - 226.0 (48.7)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1.1"
D91V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MYPOP MUTATED          0       0       1        1        0        2         0
  MYPOP WILD-TYPE       10       6      24        9       25       16        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MYPOP MUTATED           0         0         0          1          1
  MYPOP WILD-TYPE        14        10        36         13         25
                 vv
clus              STAGE IIIC STAGE IV
  MYPOP MUTATED            1        0
  MYPOP WILD-TYPE         42       16
D91V4, multiclass
            clus
vv           MYPOP MUTATED MYPOP WILD-TYPE
  I/II NOS               0              10
  STAGE 0                0               6
  STAGE I                1              24
  STAGE IA               1               9
  STAGE IB               0              25
  STAGE II               2              16
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              0              36
  STAGE IIIA             1              13
  STAGE IIIB             1              25
  STAGE IIIC             1              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
  MYPOP MUTATED       2  0  5  0
  MYPOP WILD-TYPE    51 62 55 55
D91V5, multiclass
       clus
vv      MYPOP MUTATED MYPOP WILD-TYPE
  T0+T1             2              51
  T2                0              62
  T3                5              55
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MYPOP MUTATED     4   3   0   0
  MYPOP WILD-TYPE 139  50  34  35
D91V6, multiclass
    clus
vv   MYPOP MUTATED MYPOP WILD-TYPE
  N0             4             139
  N1             3              50
  N2             0              34
  N3             0              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"
D91V7, binary
                 cls
clus                0   1
  MYPOP MUTATED     7   0
  MYPOP WILD-TYPE 249  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYPOP MUTATED      7    0
  MYPOP WILD-TYPE  249   17
   clus
vv  MYPOP MUTATED MYPOP WILD-TYPE
  0             7             249
  1             0              17
[1] 2 2
[1] FALSE
D91V8, binary
                 cls
clus                0   1
  MYPOP MUTATED     3   2
  MYPOP WILD-TYPE 104  71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYPOP MUTATED      3    2
  MYPOP WILD-TYPE  104   71
     clus
vv    MYPOP MUTATED MYPOP WILD-TYPE
  NO              3             104
  YES             2              71
[1] 2 2
[1] FALSE
D91V9, binary
                 cls
clus                0   1
  MYPOP MUTATED     0   7
  MYPOP WILD-TYPE  37 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYPOP MUTATED      0    7
  MYPOP WILD-TYPE   37  246
     clus
vv    MYPOP MUTATED MYPOP WILD-TYPE
  NO              0              37
  YES             7             246
[1] 2 2
[1] FALSE
D91V10, continuous
D91V11, binary
                 cls
clus                0   1
  MYPOP MUTATED     2   5
  MYPOP WILD-TYPE 107 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYPOP MUTATED      2    5
  MYPOP WILD-TYPE  107  176
        clus
vv       MYPOP MUTATED MYPOP WILD-TYPE
  FEMALE             2             107
  MALE               5             176
[1] 2 2
[1] FALSE
D91V12, binary
                 cls
clus                0   1
  MYPOP MUTATED     7   0
  MYPOP WILD-TYPE 247  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYPOP MUTATED      7    0
  MYPOP WILD-TYPE  247   35
     clus
vv    MYPOP MUTATED MYPOP WILD-TYPE
  NO              7             247
  YES             0              35
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYPOP MUTATED       1                         0     6
  MYPOP WILD-TYPE     4                         1   278
D91V13, multiclass
                           clus
vv                          MYPOP MUTATED MYPOP WILD-TYPE
  ASIAN                                 1               4
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 6             278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V14, binary
                 cls
clus                0   1
  MYPOP MUTATED     0   6
  MYPOP WILD-TYPE   3 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYPOP MUTATED      0    6
  MYPOP WILD-TYPE    3  277
                        clus
vv                       MYPOP MUTATED MYPOP WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             277
[1] 2 2
[1] FALSE

Clustering(92) Variable = MLL4 MUTATION ANALYSIS
D92V1, survival
                sevent
clus2             0  1
  MLL4 MUTATED   17  8
  MLL4 WILD-TYPE 80 95
  MLL4 MUTATED MLL4 WILD-TYPE 
            25            175 
  MLL4 MUTATED MLL4 WILD-TYPE 
             8             95 
$`MLL4 MUTATED`
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2JH TCGA-D3-A3MR TCGA-D3-A51R 
      134.40        19.04        36.85        36.30        90.21        62.70 
TCGA-D3-A5GL TCGA-DA-A1HY TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M 
       42.05       138.67        76.14        12.99         0.26        47.74 
TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MT TCGA-EE-A3AC 
       27.16        30.02       103.13        23.77        23.51        64.04 
TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F9 
      111.85       135.98       130.95       136.27         3.06        13.28 
TCGA-GN-A4U4 
       34.49 

$`MLL4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.90        27.35         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       40.01        59.70        24.53         9.34        23.67       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR 
       30.67       144.46        31.76        11.34        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I1 
       15.02        22.29        69.21        22.85        76.34        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T 
       79.20        75.22        44.28        47.41        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      185.19       115.43        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF 
        0.20        71.31        81.99        15.25         5.75       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      227.01       143.93        53.26       124.31       122.73         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       54.51         6.28        67.89        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       19.86        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZT 
       32.78        43.92         7.82        36.33        78.61        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        18.51        66.67       173.19 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
        7.59       120.53        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  MLL4 MUTATED MLL4 WILD-TYPE 
          0.26           0.00 
  MLL4 MUTATED MLL4 WILD-TYPE 
        138.67         346.49 
  MLL4 MUTATED MLL4 WILD-TYPE 
         42.05          47.41 
[1] "0.3 - 138.7 (42.0)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.4"
D92V2, survival
                sevent
clus2              0   1
  MLL4 MUTATED    18  13
  MLL4 WILD-TYPE 106 147
  MLL4 MUTATED MLL4 WILD-TYPE 
            31            253 
  MLL4 MUTATED MLL4 WILD-TYPE 
            13            147 
$`MLL4 MUTATED`
TCGA-D3-A3ML TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2JH TCGA-D3-A3MR 
       13.87       134.40        31.40        36.95        42.08       103.59 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-DA-A1HY TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       63.81       125.79       144.89        78.97        13.97        63.78 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2M6 TCGA-EE-A2MC 
       56.84        56.42        59.64        48.72       129.27        61.51 
TCGA-EE-A2MD TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JI 
       47.28        71.21        64.04       138.81       127.20       152.81 
TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F9 TCGA-FS-A4FB 
       23.93       133.55       148.80        27.02        34.03        26.73 
TCGA-GN-A4U4 
       39.35 

$`MLL4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A198 
      168.26         2.60       340.14       126.81        27.35        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       11.87       113.52        12.10       171.58        66.48        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-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-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-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       25.18        77.56        22.95        76.57        36.03        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       13.55        63.35        85.08        72.07        64.64        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       173.79       220.24       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF 
       94.82        21.67        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       180.39       216.66 
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-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        28.77        54.51        13.81        41.59 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       134.33        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        46.45         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-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD 
       77.82        66.67        28.73       174.84        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 
       64.44        62.79        32.48        48.00       121.91        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  MLL4 MUTATED MLL4 WILD-TYPE 
         13.87           0.20 
  MLL4 MUTATED MLL4 WILD-TYPE 
        152.81         369.93 
  MLL4 MUTATED MLL4 WILD-TYPE 
         61.51          53.19 
[1] "13.9 - 152.8 (61.5)" "0.2 - 369.9 (53.2)" 
[1] "hr=" "1.4"
D92V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MLL4 MUTATED          2       0       5        1        5        4         2
  MLL4 WILD-TYPE        8       6      20        9       20       14         8
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MLL4 MUTATED           2         1         5          1          1          3
  MLL4 WILD-TYPE        12         9        31         13         25         40
                vv
clus             STAGE IV
  MLL4 MUTATED          0
  MLL4 WILD-TYPE       16
D92V4, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  I/II NOS              2              8
  STAGE 0               0              6
  STAGE I               5             20
  STAGE IA              1              9
  STAGE IB              5             20
  STAGE II              4             14
  STAGE IIA             2              8
  STAGE IIB             2             12
  STAGE IIC             1              9
  STAGE III             5             31
  STAGE IIIA            1             13
  STAGE IIIB            1             25
  STAGE IIIC            3             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
  MLL4 MUTATED       5 12  9  4
  MLL4 WILD-TYPE    48 50 51 51
D92V5, multiclass
       clus
vv      MLL4 MUTATED MLL4 WILD-TYPE
  T0+T1            5             48
  T2              12             50
  T3               9             51
  T4               4             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLL4 MUTATED    21   6   3   1
  MLL4 WILD-TYPE 122  47  31  34
D92V6, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           21            122
  N1            6             47
  N2            3             31
  N3            1             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"
D92V7, binary
                cls
clus               0   1
  MLL4 MUTATED    32   0
  MLL4 WILD-TYPE 224  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     32    0
  MLL4 WILD-TYPE  224   17
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           32            224
  1            0             17
[1] 2 2
[1] FALSE
D92V8, binary
                cls
clus              0  1
  MLL4 MUTATED   15  9
  MLL4 WILD-TYPE 92 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     15    9
  MLL4 WILD-TYPE   92   64
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            15             92
  YES            9             64
[1] 2 2
[1] FALSE
D92V9, binary
                cls
clus               0   1
  MLL4 MUTATED     2  30
  MLL4 WILD-TYPE  35 223
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      2   30
  MLL4 WILD-TYPE   35  223
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO             2             35
  YES           30            223
[1] 2 2
[1] FALSE
D92V10, continuous
D92V11, binary
                cls
clus               0   1
  MLL4 MUTATED     5  27
  MLL4 WILD-TYPE 104 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      5   27
  MLL4 WILD-TYPE  104  154
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE            5            104
  MALE             27            154
[1] 2 2
[1] FALSE
D92V12, binary
                cls
clus               0   1
  MLL4 MUTATED    25   7
  MLL4 WILD-TYPE 229  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     25    7
  MLL4 WILD-TYPE  229   28
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            25            229
  YES            7             28
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED       0                         0    32
  MLL4 WILD-TYPE     5                         1   252
D92V13, multiclass
                           clus
vv                          MLL4 MUTATED MLL4 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               32            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"
D92V14, binary
                cls
clus               0   1
  MLL4 MUTATED     1  31
  MLL4 WILD-TYPE   2 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      1   31
  MLL4 WILD-TYPE    2  252
                        clus
vv                       MLL4 MUTATED MLL4 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           31            252
[1] 2 2
[1] FALSE

Clustering(93) Variable = MMP1 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2             0  1
  MMP1 MUTATED    6  7
  MMP1 WILD-TYPE 91 96
  MMP1 MUTATED MMP1 WILD-TYPE 
            13            187 
  MMP1 MUTATED MMP1 WILD-TYPE 
             7             96 
$`MMP1 MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A51F TCGA-D9-A6EC 
      166.75        52.90        19.04        36.85        30.67        69.21 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A2MU TCGA-EE-A3JI TCGA-FS-A1Z3 
       13.15        26.24        75.55        53.26       135.98         8.35 
TCGA-FS-A4F0 
       18.51 

$`MMP1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        38.76        33.24        31.96       269.03       134.40 
TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       27.35         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV 
       45.70       177.86        15.02        22.29        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20F 
       52.41        18.21        24.89        20.38         0.00        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01       143.93        23.51       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35       168.85        19.86        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        5.29         3.06        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  MMP1 MUTATED MMP1 WILD-TYPE 
          8.35           0.00 
  MMP1 MUTATED MMP1 WILD-TYPE 
        166.75         346.49 
  MMP1 MUTATED MMP1 WILD-TYPE 
         36.85          47.41 
[1] "8.3 - 166.8 (36.9)" "0.0 - 346.5 (47.4)"
[1] "hr=" "1.3"
D93V2, survival
                sevent
clus2              0   1
  MMP1 MUTATED     6   8
  MMP1 WILD-TYPE 118 152
  MMP1 MUTATED MMP1 WILD-TYPE 
            14            270 
  MMP1 MUTATED MMP1 WILD-TYPE 
             8            152 
$`MMP1 MUTATED`
TCGA-EE-A20H TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A51F TCGA-D9-A6EC 
      168.26       126.81        31.40        36.95        55.73        77.56 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A2MU TCGA-EE-A3AH TCGA-EE-A3JI 
       29.82        26.89       151.27        53.26       138.81       152.81 
TCGA-FS-A1Z3 TCGA-FS-A4F0 
       20.91        77.82 

$`MMP1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 
       68.15         2.60       340.14       134.40        27.35        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       45.30       174.84        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       15.39        22.29         9.90        25.18        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       20.35        29.29        58.92         7.04        36.46        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        8.65        33.73        14.70         4.96       133.81        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23       162.48        71.21       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       64.04        28.77        54.51        13.81        41.59       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-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       134.33        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.48        27.09        27.02        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  MMP1 MUTATED MMP1 WILD-TYPE 
         20.91           0.20 
  MMP1 MUTATED MMP1 WILD-TYPE 
        168.26         369.93 
  MMP1 MUTATED MMP1 WILD-TYPE 
        66.645         53.720 
[1] "20.9 - 168.3 (66.6)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1.1"
D93V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MMP1 MUTATED          0       2       2        2        0        2         0
  MMP1 WILD-TYPE       10       4      23        8       25       16        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MMP1 MUTATED           2         0         1          1          0          1
  MMP1 WILD-TYPE        12        10        35         13         26         42
                vv
clus             STAGE IV
  MMP1 MUTATED          1
  MMP1 WILD-TYPE       15
D93V4, multiclass
            clus
vv           MMP1 MUTATED MMP1 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               2              4
  STAGE I               2             23
  STAGE IA              2              8
  STAGE IB              0             25
  STAGE II              2             16
  STAGE IIA             0             10
  STAGE IIB             2             12
  STAGE IIC             0             10
  STAGE III             1             35
  STAGE IIIA            1             13
  STAGE IIIB            0             26
  STAGE IIIC            1             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
  MMP1 MUTATED       2  2  4  2
  MMP1 WILD-TYPE    51 60 56 53
D93V5, multiclass
       clus
vv      MMP1 MUTATED MMP1 WILD-TYPE
  T0+T1            2             51
  T2               2             60
  T3               4             56
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MMP1 MUTATED    11   2   1   0
  MMP1 WILD-TYPE 132  51  33  35
D93V6, multiclass
    clus
vv   MMP1 MUTATED MMP1 WILD-TYPE
  N0           11            132
  N1            2             51
  N2            1             33
  N3            0             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"
D93V7, binary
                cls
clus               0   1
  MMP1 MUTATED    13   1
  MMP1 WILD-TYPE 243  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED     13    1
  MMP1 WILD-TYPE  243   16
   clus
vv  MMP1 MUTATED MMP1 WILD-TYPE
  0           13            243
  1            1             16
[1] 2 2
[1] FALSE
D93V8, binary
                cls
clus              0  1
  MMP1 MUTATED    8  1
  MMP1 WILD-TYPE 99 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      8    1
  MMP1 WILD-TYPE   99   72
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  NO             8             99
  YES            1             72
[1] 2 2
[1] FALSE
D93V9, binary
                cls
clus               0   1
  MMP1 MUTATED     1  13
  MMP1 WILD-TYPE  36 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      1   13
  MMP1 WILD-TYPE   36  240
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  NO             1             36
  YES           13            240
[1] 2 2
[1] FALSE
D93V10, continuous
D93V11, binary
                cls
clus               0   1
  MMP1 MUTATED     3  11
  MMP1 WILD-TYPE 106 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      3   11
  MMP1 WILD-TYPE  106  170
        clus
vv       MMP1 MUTATED MMP1 WILD-TYPE
  FEMALE            3            106
  MALE             11            170
[1] 2 2
[1] FALSE
D93V12, binary
                cls
clus               0   1
  MMP1 MUTATED    13   1
  MMP1 WILD-TYPE 241  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED     13    1
  MMP1 WILD-TYPE  241   34
     clus
vv    MMP1 MUTATED MMP1 WILD-TYPE
  NO            13            241
  YES            1             34
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP1 MUTATED       0                         0    14
  MMP1 WILD-TYPE     5                         1   270
D93V13, multiclass
                           clus
vv                          MMP1 MUTATED MMP1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               14            270
[1] 3 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
  MMP1 MUTATED     0  13
  MMP1 WILD-TYPE   3 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP1 MUTATED      0   13
  MMP1 WILD-TYPE    3  270
                        clus
vv                       MMP1 MUTATED MMP1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13            270
[1] 2 2
[1] FALSE

Clustering(94) Variable = THEMIS MUTATION ANALYSIS
D94V1, survival
                  sevent
clus2               0  1
  THEMIS MUTATED   15  7
  THEMIS WILD-TYPE 82 96
  THEMIS MUTATED THEMIS WILD-TYPE 
              22              178 
  THEMIS MUTATED THEMIS WILD-TYPE 
               7               96 
$`THEMIS MUTATED`
TCGA-EE-A180 TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1QA TCGA-D3-A2JL 
       31.96        52.90        19.04        36.85        76.41       171.58 
TCGA-D3-A2JO TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       66.08        76.34        13.15        76.14        12.99        47.41 
TCGA-EE-A29Q TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-ER-A19A TCGA-ER-A19S 
       61.12       143.93        54.51        45.90         4.54        47.18 
TCGA-ER-A42L TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-QB-A6FS 
       74.47        13.28        80.68         7.23 

$`THEMIS WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        38.76        33.24       166.75       269.03       134.40 
TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       27.35         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        19.04        62.60        25.64        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JN 
       15.75       168.00        86.30       107.61        36.30        64.83 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        22.29        69.21        22.85       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       75.22         0.26        44.28        47.74        27.16       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU 
       89.26       104.78       145.45       227.01        23.51        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J3 
      124.31       122.73        64.04         4.41         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
      111.85         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
       10.49         7.82        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       28.67       173.29        68.52        15.48        32.05         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-FW-A3TV 
        3.06        18.51        66.67       173.19        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         0.20         0.33 

  THEMIS MUTATED THEMIS WILD-TYPE 
            4.54             0.00 
  THEMIS MUTATED THEMIS WILD-TYPE 
          171.58           346.49 
  THEMIS MUTATED THEMIS WILD-TYPE 
          50.155           46.455 
[1] "4.5 - 171.6 (50.2)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.4"
D94V2, survival
                  sevent
clus2                0   1
  THEMIS MUTATED    18  15
  THEMIS WILD-TYPE 106 145
  THEMIS MUTATED THEMIS WILD-TYPE 
              33              251 
  THEMIS MUTATED THEMIS WILD-TYPE 
              15              145 
$`THEMIS MUTATED`
TCGA-D3-A3ML TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2GO TCGA-ER-A193 TCGA-FW-A3R5 
       13.87        94.98         2.60       126.81        31.40        36.95 
TCGA-D3-A1QA TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A3F3 
       90.90       171.58        66.08       137.92        76.57        10.49 
TCGA-EE-A17X TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A2GC 
       29.82        78.97        13.97        64.64        66.74        67.43 
TCGA-EE-A2M5 TCGA-EE-A2MS TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 
       21.67       162.48        54.51       138.81        36.95        64.08 
TCGA-EE-A3JA TCGA-ER-A19A TCGA-ER-A19S TCGA-ER-A42L TCGA-FS-A1ZA TCGA-FS-A4F9 
       53.19        77.75        49.48       149.03        27.72        34.03 
TCGA-FS-A4FD TCGA-GF-A6C9 TCGA-QB-A6FS 
       80.68        15.78         7.23 

$`THEMIS WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20H 
       62.07        46.32        68.25        54.02        68.15       168.26 
TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 
      340.14       134.40        27.35        50.76        15.45        16.57 
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-A2JG TCGA-D3-A2JH 
      115.53       168.00        86.76        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10        66.48        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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-D9-A6EC 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        33.93       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y 
       20.35        29.29        58.92         7.04        36.46        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E 
      151.27        91.56        13.55        63.35        85.08        63.78 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       72.07        56.84        18.61        56.42        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       59.64        39.29        86.14        59.28       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        42.77        81.21        44.88        94.82       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       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        64.04        28.77        13.81        41.59 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
      172.18       127.20        34.32       201.80        51.35       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
      152.81        35.44        13.94         9.17        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       302.07       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
      131.51        61.05        44.09       162.08        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       12.95        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        54.41        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         0.20         0.33         0.69 

  THEMIS MUTATED THEMIS WILD-TYPE 
             2.6              0.2 
  THEMIS MUTATED THEMIS WILD-TYPE 
          171.58           369.93 
  THEMIS MUTATED THEMIS WILD-TYPE 
           64.08            53.52 
[1] "2.6 - 171.6 (64.1)" "0.2 - 369.9 (53.5)"
[1] "hr=" "1.1"
D94V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  THEMIS MUTATED          1       1       2        3        3        5
  THEMIS WILD-TYPE        9       5      23        7       22       13
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  THEMIS MUTATED           0         3         0         3          1
  THEMIS WILD-TYPE        10        11        10        33         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  THEMIS MUTATED            4          6        1
  THEMIS WILD-TYPE         22         37       15
D94V4, multiclass
            clus
vv           THEMIS MUTATED THEMIS WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 1                5
  STAGE I                 2               23
  STAGE IA                3                7
  STAGE IB                3               22
  STAGE II                5               13
  STAGE IIA               0               10
  STAGE IIB               3               11
  STAGE IIC               0               10
  STAGE III               3               33
  STAGE IIIA              1               13
  STAGE IIIB              4               22
  STAGE IIIC              6               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
  THEMIS MUTATED       6  6  9  6
  THEMIS WILD-TYPE    47 56 51 49
D94V5, multiclass
       clus
vv      THEMIS MUTATED THEMIS WILD-TYPE
  T0+T1              6               47
  T2                 6               56
  T3                 9               51
  T4                 6               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  THEMIS MUTATED    20   2   5   5
  THEMIS WILD-TYPE 123  51  29  30
D94V6, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  N0             20              123
  N1              2               51
  N2              5               29
  N3              5               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"
D94V7, binary
                  cls
clus                 0   1
  THEMIS MUTATED    31   1
  THEMIS WILD-TYPE 225  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     31    1
  THEMIS WILD-TYPE  225   16
   clus
vv  THEMIS MUTATED THEMIS WILD-TYPE
  0             31              225
  1              1               16
[1] 2 2
[1] FALSE
D94V8, binary
                  cls
clus                0  1
  THEMIS MUTATED   15  8
  THEMIS WILD-TYPE 92 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     15    8
  THEMIS WILD-TYPE   92   65
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO              15               92
  YES              8               65
[1] 2 2
[1] FALSE
D94V9, binary
                  cls
clus                 0   1
  THEMIS MUTATED     6  28
  THEMIS WILD-TYPE  31 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      6   28
  THEMIS WILD-TYPE   31  225
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO               6               31
  YES             28              225
[1] 2 2
[1] FALSE
D94V10, continuous
D94V11, binary
                  cls
clus                 0   1
  THEMIS MUTATED     9  25
  THEMIS WILD-TYPE 100 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      9   25
  THEMIS WILD-TYPE  100  156
        clus
vv       THEMIS MUTATED THEMIS WILD-TYPE
  FEMALE              9              100
  MALE               25              156
[1] 2 2
[1] FALSE
D94V12, binary
                  cls
clus                 0   1
  THEMIS MUTATED    32   2
  THEMIS WILD-TYPE 222  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     32    2
  THEMIS WILD-TYPE  222   33
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO              32              222
  YES              2               33
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THEMIS MUTATED       0                         0    34
  THEMIS WILD-TYPE     5                         1   250
D94V13, multiclass
                           clus
vv                          THEMIS MUTATED THEMIS WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 34              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"
D94V14, binary
                  cls
clus                 0   1
  THEMIS MUTATED     0  33
  THEMIS WILD-TYPE   3 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      0   33
  THEMIS WILD-TYPE    3  250
                        clus
vv                       THEMIS MUTATED THEMIS WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             33              250
[1] 2 2
[1] FALSE

Clustering(95) Variable = ACO1 MUTATION ANALYSIS
D95V1, survival
                sevent
clus2              0   1
  ACO1 MUTATED     4   3
  ACO1 WILD-TYPE  93 100
  ACO1 MUTATED ACO1 WILD-TYPE 
             7            193 
  ACO1 MUTATED ACO1 WILD-TYPE 
             3            100 
$`ACO1 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29D TCGA-EE-A29M TCGA-ER-A19P TCGA-FS-A1ZM TCGA-FS-A1ZZ 
       76.34        12.99        47.74       120.76        78.61         3.06 
TCGA-QB-A6FS 
        7.23 

$`ACO1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
      177.86        15.02        22.29        69.21        22.85       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        75.22        76.14         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.82        36.33       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       23.21         5.29        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 
        7.59       120.53        34.49        46.92       297.01         0.20 
TCGA-RP-A693 
        0.33 

  ACO1 MUTATED ACO1 WILD-TYPE 
          3.06           0.00 
  ACO1 MUTATED ACO1 WILD-TYPE 
        120.76         346.49 
  ACO1 MUTATED ACO1 WILD-TYPE 
         47.74          47.18 
[1] "3.1 - 120.8 (47.7)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.1"
D95V2, survival
                sevent
clus2              0   1
  ACO1 MUTATED     4   4
  ACO1 WILD-TYPE 120 156
  ACO1 MUTATED ACO1 WILD-TYPE 
             8            276 
  ACO1 MUTATED ACO1 WILD-TYPE 
             4            156 
$`ACO1 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29D TCGA-EE-A29M TCGA-ER-A19P TCGA-ER-A42K TCGA-FS-A1ZM 
       76.57        13.97        56.84       162.08        12.95       101.26 
TCGA-FS-A1ZZ TCGA-QB-A6FS 
       27.02         7.23 

$`ACO1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29         9.90        25.18        77.56        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        18.61        56.42        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        44.09        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       41.56       247.04        93.01        46.98        33.21       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       48.89        22.13       297.90         0.20         0.33         0.69 

  ACO1 MUTATED ACO1 WILD-TYPE 
          7.23           0.20 
  ACO1 MUTATED ACO1 WILD-TYPE 
        162.08         369.93 
  ACO1 MUTATED ACO1 WILD-TYPE 
         41.93          53.97 
[1] "7.2 - 162.1 (41.9)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1.2"
D95V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ACO1 MUTATED          0       0       0        0        1        0         0
  ACO1 WILD-TYPE       10       6      25       10       24       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ACO1 MUTATED           1         0         1          0          1          3
  ACO1 WILD-TYPE        13        10        35         14         25         40
                vv
clus             STAGE IV
  ACO1 MUTATED          0
  ACO1 WILD-TYPE       16
D95V4, multiclass
            clus
vv           ACO1 MUTATED ACO1 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               0             25
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             1             13
  STAGE IIC             0             10
  STAGE III             1             35
  STAGE IIIA            0             14
  STAGE IIIB            1             25
  STAGE IIIC            3             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
  ACO1 MUTATED       2  2  2  1
  ACO1 WILD-TYPE    51 60 58 54
D95V5, multiclass
       clus
vv      ACO1 MUTATED ACO1 WILD-TYPE
  T0+T1            2             51
  T2               2             60
  T3               2             58
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ACO1 MUTATED     3   1   2   2
  ACO1 WILD-TYPE 140  52  32  33
D95V6, multiclass
    clus
vv   ACO1 MUTATED ACO1 WILD-TYPE
  N0            3            140
  N1            1             52
  N2            2             32
  N3            2             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"
D95V7, binary
                cls
clus               0   1
  ACO1 MUTATED     8   0
  ACO1 WILD-TYPE 248  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACO1 MUTATED      8    0
  ACO1 WILD-TYPE  248   17
   clus
vv  ACO1 MUTATED ACO1 WILD-TYPE
  0            8            248
  1            0             17
[1] 2 2
[1] FALSE
D95V8, binary
                cls
clus               0   1
  ACO1 MUTATED     1   3
  ACO1 WILD-TYPE 106  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACO1 MUTATED      1    3
  ACO1 WILD-TYPE  106   70
     clus
vv    ACO1 MUTATED ACO1 WILD-TYPE
  NO             1            106
  YES            3             70
[1] 2 2
[1] FALSE
D95V9, binary
                cls
clus               0   1
  ACO1 MUTATED     2   6
  ACO1 WILD-TYPE  35 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACO1 MUTATED      2    6
  ACO1 WILD-TYPE   35  247
     clus
vv    ACO1 MUTATED ACO1 WILD-TYPE
  NO             2             35
  YES            6            247
[1] 2 2
[1] FALSE
D95V10, continuous
D95V11, binary
                cls
clus               0   1
  ACO1 MUTATED     5   3
  ACO1 WILD-TYPE 104 178
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACO1 MUTATED      5    3
  ACO1 WILD-TYPE  104  178
        clus
vv       ACO1 MUTATED ACO1 WILD-TYPE
  FEMALE            5            104
  MALE              3            178
[1] 2 2
[1] FALSE
D95V12, binary
                cls
clus               0   1
  ACO1 MUTATED     7   1
  ACO1 WILD-TYPE 247  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACO1 MUTATED      7    1
  ACO1 WILD-TYPE  247   34
     clus
vv    ACO1 MUTATED ACO1 WILD-TYPE
  NO             7            247
  YES            1             34
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACO1 MUTATED       0                         0     8
  ACO1 WILD-TYPE     5                         1   276
D95V13, multiclass
                           clus
vv                          ACO1 MUTATED ACO1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                8            276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V14, binary
                cls
clus               0   1
  ACO1 MUTATED     1   7
  ACO1 WILD-TYPE   2 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACO1 MUTATED      1    7
  ACO1 WILD-TYPE    2  276
                        clus
vv                       ACO1 MUTATED ACO1 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            7            276
[1] 2 2
[1] FALSE

Clustering(96) Variable = MUC7 MUTATION ANALYSIS
D96V1, survival
                sevent
clus2             0  1
  MUC7 MUTATED    5  5
  MUC7 WILD-TYPE 92 98
  MUC7 MUTATED MUC7 WILD-TYPE 
            10            190 
  MUC7 MUTATED MUC7 WILD-TYPE 
             5             98 
$`MUC7 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-D9-A6EC TCGA-DA-A1IC TCGA-EE-A181 
       52.90       134.40        27.35        69.21        58.85        20.38 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GJ TCGA-EE-A2MS 
       12.99         0.26        68.65       143.93 

$`MUC7 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       19.04        36.85         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       60.10        64.83        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
       26.24        75.55        79.20        75.22        76.14        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  MUC7 MUTATED MUC7 WILD-TYPE 
          0.26           0.00 
  MUC7 MUTATED MUC7 WILD-TYPE 
        143.93         346.49 
  MUC7 MUTATED MUC7 WILD-TYPE 
        55.875         47.050 
[1] "0.3 - 143.9 (55.9)" "0.0 - 346.5 (47.0)"
[1] "hr=" "1.2"
D96V2, survival
                sevent
clus2              0   1
  MUC7 MUTATED     8   9
  MUC7 WILD-TYPE 116 151
  MUC7 MUTATED MUC7 WILD-TYPE 
            17            267 
  MUC7 MUTATED MUC7 WILD-TYPE 
             9            151 
$`MUC7 MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1IC 
      126.81       134.40        27.35       137.92        77.56        68.09 
TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2MS 
       33.73        13.97        63.78        67.43       107.38       162.48 
TCGA-EE-A3J5 TCGA-FS-A1ZK TCGA-FS-A4FC TCGA-GF-A6C9 TCGA-GN-A4U7 
       36.95        23.93        54.41        15.78        10.42 

$`MUC7 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-ER-A193 TCGA-ER-A198 
       68.15       168.26         2.60       340.14        31.40        50.76 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       15.45        36.95        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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-D9-A6EG 
        7.10        15.39        22.29         9.90        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        14.70        26.89         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        85.08        78.97 
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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24        48.72        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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 
      180.39       216.66       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       138.81       172.18       127.20 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         9.70        32.75        47.38       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       34.03        26.73        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        19.43         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
      121.91        39.35        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  MUC7 MUTATED MUC7 WILD-TYPE 
         10.42           0.20 
  MUC7 MUTATED MUC7 WILD-TYPE 
        162.48         369.93 
  MUC7 MUTATED MUC7 WILD-TYPE 
         63.78          53.52 
[1] "10.4 - 162.5 (63.8)" "0.2 - 369.9 (53.5)" 
[1] "hr=" "1"  
D96V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MUC7 MUTATED          0       0       1        1        0        5         1
  MUC7 WILD-TYPE       10       6      24        9       25       13         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MUC7 MUTATED           1         0         2          1          3          2
  MUC7 WILD-TYPE        13        10        34         13         23         41
                vv
clus             STAGE IV
  MUC7 MUTATED          0
  MUC7 WILD-TYPE       16
D96V4, multiclass
            clus
vv           MUC7 MUTATED MUC7 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               1             24
  STAGE IA              1              9
  STAGE IB              0             25
  STAGE II              5             13
  STAGE IIA             1              9
  STAGE IIB             1             13
  STAGE IIC             0             10
  STAGE III             2             34
  STAGE IIIA            1             13
  STAGE IIIB            3             23
  STAGE IIIC            2             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
  MUC7 MUTATED       1  2  9  3
  MUC7 WILD-TYPE    52 60 51 52
D96V5, multiclass
       clus
vv      MUC7 MUTATED MUC7 WILD-TYPE
  T0+T1            1             52
  T2               2             60
  T3               9             51
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MUC7 MUTATED     9   4   2   1
  MUC7 WILD-TYPE 134  49  32  34
D96V6, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  N0            9            134
  N1            4             49
  N2            2             32
  N3            1             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"
D96V7, binary
                cls
clus               0   1
  MUC7 MUTATED    16   0
  MUC7 WILD-TYPE 240  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED     16    0
  MUC7 WILD-TYPE  240   17
   clus
vv  MUC7 MUTATED MUC7 WILD-TYPE
  0           16            240
  1            0             17
[1] 2 2
[1] FALSE
D96V8, binary
                cls
clus              0  1
  MUC7 MUTATED   10  2
  MUC7 WILD-TYPE 97 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED     10    2
  MUC7 WILD-TYPE   97   71
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO            10             97
  YES            2             71
[1] 2 2
[1] FALSE
D96V9, binary
                cls
clus               0   1
  MUC7 MUTATED     2  15
  MUC7 WILD-TYPE  35 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      2   15
  MUC7 WILD-TYPE   35  238
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO             2             35
  YES           15            238
[1] 2 2
[1] FALSE
D96V10, continuous
D96V11, binary
                cls
clus               0   1
  MUC7 MUTATED     4  13
  MUC7 WILD-TYPE 105 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      4   13
  MUC7 WILD-TYPE  105  168
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  FEMALE            4            105
  MALE             13            168
[1] 2 2
[1] FALSE
D96V12, binary
                cls
clus               0   1
  MUC7 MUTATED    15   2
  MUC7 WILD-TYPE 239  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED     15    2
  MUC7 WILD-TYPE  239   33
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO            15            239
  YES            2             33
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC7 MUTATED       0                         0    17
  MUC7 WILD-TYPE     5                         1   267
D96V13, multiclass
                           clus
vv                          MUC7 MUTATED MUC7 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               17            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"
D96V14, binary
                cls
clus               0   1
  MUC7 MUTATED     0  17
  MUC7 WILD-TYPE   3 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      0   17
  MUC7 WILD-TYPE    3  266
                        clus
vv                       MUC7 MUTATED MUC7 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           17            266
[1] 2 2
[1] FALSE

Clustering(97) Variable = TP63 MUTATION ANALYSIS
D97V1, survival
                sevent
clus2             0  1
  TP63 MUTATED   16 17
  TP63 WILD-TYPE 81 86
  TP63 MUTATED TP63 WILD-TYPE 
            33            167 
  TP63 MUTATED TP63 WILD-TYPE 
            17             86 
$`TP63 MUTATED`
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A3MU TCGA-D3-A51R 
      134.40        27.35        19.04        36.85        23.67        62.70 
TCGA-D3-A51T TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-EE-A181 
       11.34        22.29        69.21        22.85        76.34        20.38 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A2GR 
       76.14         0.26        47.41        47.74        26.14         0.20 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A3AF 
       23.77       171.85        63.25        89.26       104.78         6.28 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-FR-A3YN TCGA-FS-A1ZE TCGA-FS-A1ZZ TCGA-FW-A3TU 
        3.35       135.98         4.50        43.92         3.06        55.59 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A267 
       18.25         1.91        17.06 

$`TP63 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       52.90         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E 
       40.01        59.70        24.53         9.34        90.21       173.85 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       30.67       144.46        31.76        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       15.02       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
       26.24        75.55        79.20        75.22        12.99        44.28 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35        93.63         0.76        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP 
       15.25         5.75       209.79        94.19       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
        4.41        54.51        67.89       111.85        45.90       168.85 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       19.86        34.45        10.49         7.82         4.54        53.29 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M 
       39.81        11.47       184.60       150.12        99.06        59.84 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.51       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1YW 
       68.52        15.48        32.05        74.47       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
       13.28        80.68        11.54        19.30         9.90        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        96.92        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  TP63 MUTATED TP63 WILD-TYPE 
           0.2            0.0 
  TP63 MUTATED TP63 WILD-TYPE 
        171.85         346.49 
  TP63 MUTATED TP63 WILD-TYPE 
         26.14          52.41 
[1] "0.2 - 171.8 (26.1)" "0.0 - 346.5 (52.4)"
[1] "hr=" "1.6"
D97V2, survival
                sevent
clus2              0   1
  TP63 MUTATED    22  27
  TP63 WILD-TYPE 102 133
  TP63 MUTATED TP63 WILD-TYPE 
            49            235 
  TP63 MUTATED TP63 WILD-TYPE 
            27            133 
$`TP63 MUTATED`
TCGA-D3-A3ML TCGA-EE-A29L TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 
       13.87         2.60       134.40        27.35        31.40        36.95 
TCGA-D3-A2JK TCGA-D3-A3C7 TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO 
       12.10        46.98        39.75        63.81        26.89       137.92 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A29C 
       22.29        77.56        22.95        76.57        33.73        78.97 
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        42.77        21.67        61.51        47.28       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A3AF TCGA-EE-A3J8 TCGA-EE-A3JI 
       96.23       180.39       216.66        13.81        34.32       152.81 
TCGA-ER-A19F TCGA-FR-A3YN TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZZ 
       26.37        92.98         7.79        27.72        46.45        27.02 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 
       55.59        19.43         2.04        15.78        10.13        64.44 
TCGA-RP-A694 
        0.69 

$`TP63 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 
      168.26       340.14       126.81        50.76        15.45        16.57 
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-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-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08       171.58        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       166.52        86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62       125.79       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         7.10        15.39 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        25.18        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       36.46        29.82        27.22         8.65        14.70        26.89 
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-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       85.08        13.97        72.07        56.42        66.74        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.64        39.29        86.14       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       81.21        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        64.04        28.77        54.51        41.59       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-A199 TCGA-ER-A19A 
       51.35       134.33        35.44        13.94         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       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21        12.95       149.03       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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        53.52         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A264 
       17.46        13.51        19.30         9.90       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 
        0.33 

  TP63 MUTATED TP63 WILD-TYPE 
          0.69           0.20 
  TP63 MUTATED TP63 WILD-TYPE 
        216.66         369.93 
  TP63 MUTATED TP63 WILD-TYPE 
         39.75          54.74 
[1] "0.7 - 216.7 (39.8)" "0.2 - 369.9 (54.7)"
[1] "hr=" "1.4"
D97V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  TP63 MUTATED          1       1       4        1        3        5         1
  TP63 WILD-TYPE        9       5      21        9       22       13         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TP63 MUTATED           5         1         5          6          6          7
  TP63 WILD-TYPE         9         9        31          8         20         36
                vv
clus             STAGE IV
  TP63 MUTATED          1
  TP63 WILD-TYPE       15
D97V4, multiclass
            clus
vv           TP63 MUTATED TP63 WILD-TYPE
  I/II NOS              1              9
  STAGE 0               1              5
  STAGE I               4             21
  STAGE IA              1              9
  STAGE IB              3             22
  STAGE II              5             13
  STAGE IIA             1              9
  STAGE IIB             5              9
  STAGE IIC             1              9
  STAGE III             5             31
  STAGE IIIA            6              8
  STAGE IIIB            6             20
  STAGE IIIC            7             36
  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 14
  TP63 WILD-TYPE    48 54 46 41
D97V5, multiclass
       clus
vv      TP63 MUTATED TP63 WILD-TYPE
  T0+T1            5             48
  T2               8             54
  T3              14             46
  T4              14             41
[1] 4 2
[1] TRUE
[1] "dimension of 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  11   7   3
  TP63 WILD-TYPE 119  42  27  32
D97V6, multiclass
    clus
vv   TP63 MUTATED TP63 WILD-TYPE
  N0           24            119
  N1           11             42
  N2            7             27
  N3            3             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"
D97V7, binary
                cls
clus               0   1
  TP63 MUTATED    46   1
  TP63 WILD-TYPE 210  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     46    1
  TP63 WILD-TYPE  210   16
   clus
vv  TP63 MUTATED TP63 WILD-TYPE
  0           46            210
  1            1             16
[1] 2 2
[1] FALSE
D97V8, binary
                cls
clus              0  1
  TP63 MUTATED   20 13
  TP63 WILD-TYPE 87 60
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     20   13
  TP63 WILD-TYPE   87   60
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO            20             87
  YES           13             60
[1] 2 2
[1] FALSE
D97V9, binary
                cls
clus               0   1
  TP63 MUTATED     8  42
  TP63 WILD-TYPE  29 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      8   42
  TP63 WILD-TYPE   29  211
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO             8             29
  YES           42            211
[1] 2 2
[1] FALSE
D97V10, continuous
D97V11, binary
                cls
clus               0   1
  TP63 MUTATED    15  35
  TP63 WILD-TYPE  94 146
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     15   35
  TP63 WILD-TYPE   94  146
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  FEMALE           15             94
  MALE             35            146
[1] 2 2
[1] FALSE
D97V12, binary
                cls
clus               0   1
  TP63 MUTATED    41   9
  TP63 WILD-TYPE 213  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED     41    9
  TP63 WILD-TYPE  213   26
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO            41            213
  YES            9             26
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP63 MUTATED       0                         0    50
  TP63 WILD-TYPE     5                         1   234
D97V13, multiclass
                           clus
vv                          TP63 MUTATED TP63 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               50            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"
D97V14, binary
                cls
clus               0   1
  TP63 MUTATED     1  49
  TP63 WILD-TYPE   2 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      1   49
  TP63 WILD-TYPE    2  234
                        clus
vv                       TP63 MUTATED TP63 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           49            234
[1] 2 2
[1] FALSE

Clustering(98) Variable = APCS MUTATION ANALYSIS
D98V1, survival
                sevent
clus2             0  1
  APCS MUTATED    4  5
  APCS WILD-TYPE 93 98
  APCS MUTATED APCS WILD-TYPE 
             9            191 
  APCS MUTATED APCS WILD-TYPE 
             5             98 
$`APCS MUTATED`
TCGA-D3-A2JF TCGA-FW-A3R5 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A182 TCGA-EE-A20C 
       62.07        36.85        60.10        42.64         0.00        75.55 
TCGA-EE-A2MI TCGA-FS-A1Z3 TCGA-GN-A268 
      171.85         8.35        42.48 

$`APCS WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
      134.40        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      150.61       110.53        64.83        58.85        30.44       225.11 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       20.38        26.24        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ 
       15.25         5.75        23.77       209.79        94.19        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      174.21       171.78        49.74       195.98        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
      117.93        96.92        17.06         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  APCS MUTATED APCS WILD-TYPE 
           0.0            0.2 
  APCS MUTATED APCS WILD-TYPE 
        171.85         346.49 
  APCS MUTATED APCS WILD-TYPE 
         42.64          47.41 
[1] "0.0 - 171.8 (42.6)" "0.2 - 346.5 (47.4)"
[1] "hr=" "1.3"
D98V2, survival
                sevent
clus2              0   1
  APCS MUTATED     6   6
  APCS WILD-TYPE 118 154
  APCS MUTATED APCS WILD-TYPE 
            12            272 
  APCS MUTATED APCS WILD-TYPE 
             6            154 
$`APCS MUTATED`
TCGA-D3-A2JF TCGA-FW-A3R5 TCGA-D3-A51N TCGA-D9-A148 TCGA-DA-A1I7 TCGA-DA-A3F8 
       62.07        36.95        22.62       151.53        88.87        43.36 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A2MI TCGA-ER-A19E TCGA-FS-A1Z3 TCGA-GN-A268 
       14.70       151.27       204.66        13.02        20.91        62.79 

$`APCS WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW 
      137.92       178.32        18.18       125.19        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93       135.02        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        33.93        10.49       225.96        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       27.22         8.65        33.73        26.89         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        85.08        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96        96.23       180.39       216.66       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        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       19.43         2.04        15.78       139.89       117.93        96.92 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       10.13        64.44        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  APCS MUTATED APCS WILD-TYPE 
         13.02           0.20 
  APCS MUTATED APCS WILD-TYPE 
        204.66         369.93 
  APCS MUTATED APCS WILD-TYPE 
        52.715         53.970 
[1] "13.0 - 204.7 (52.7)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1.1"
D98V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  APCS MUTATED          0       1       0        1        1        0         0
  APCS WILD-TYPE       10       5      25        9       24       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  APCS MUTATED           2         0         1          0          2          1
  APCS WILD-TYPE        12        10        35         14         24         42
                vv
clus             STAGE IV
  APCS MUTATED          3
  APCS WILD-TYPE       13
D98V4, multiclass
            clus
vv           APCS MUTATED APCS WILD-TYPE
  I/II NOS              0             10
  STAGE 0               1              5
  STAGE I               0             25
  STAGE IA              1              9
  STAGE IB              1             24
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             2             12
  STAGE IIC             0             10
  STAGE III             1             35
  STAGE IIIA            0             14
  STAGE IIIB            2             24
  STAGE IIIC            1             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
  APCS MUTATED       3  2  0  3
  APCS WILD-TYPE    50 60 60 52
D98V5, multiclass
       clus
vv      APCS MUTATED APCS WILD-TYPE
  T0+T1            3             50
  T2               2             60
  T3               0             60
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  APCS MUTATED     6   1   3   2
  APCS WILD-TYPE 137  52  31  33
D98V6, multiclass
    clus
vv   APCS MUTATED APCS WILD-TYPE
  N0            6            137
  N1            1             52
  N2            3             31
  N3            2             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"
D98V7, binary
                cls
clus               0   1
  APCS MUTATED     9   4
  APCS WILD-TYPE 247  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  APCS MUTATED      9    4
  APCS WILD-TYPE  247   13
   clus
vv  APCS MUTATED APCS WILD-TYPE
  0            9            247
  1            4             13
[1] 2 2
[1] FALSE
D98V8, binary
                cls
clus               0   1
  APCS MUTATED     5   1
  APCS WILD-TYPE 102  72
[1] "tbl2"
                cls
clus             [,1] [,2]
  APCS MUTATED      5    1
  APCS WILD-TYPE  102   72
     clus
vv    APCS MUTATED APCS WILD-TYPE
  NO             5            102
  YES            1             72
[1] 2 2
[1] FALSE
D98V9, binary
                cls
clus               0   1
  APCS MUTATED     3  10
  APCS WILD-TYPE  34 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  APCS MUTATED      3   10
  APCS WILD-TYPE   34  243
     clus
vv    APCS MUTATED APCS WILD-TYPE
  NO             3             34
  YES           10            243
[1] 2 2
[1] FALSE
D98V10, continuous
D98V11, binary
                cls
clus               0   1
  APCS MUTATED     5   8
  APCS WILD-TYPE 104 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  APCS MUTATED      5    8
  APCS WILD-TYPE  104  173
        clus
vv       APCS MUTATED APCS WILD-TYPE
  FEMALE            5            104
  MALE              8            173
[1] 2 2
[1] FALSE
D98V12, binary
                cls
clus               0   1
  APCS MUTATED    12   1
  APCS WILD-TYPE 242  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  APCS MUTATED     12    1
  APCS WILD-TYPE  242   34
     clus
vv    APCS MUTATED APCS WILD-TYPE
  NO            12            242
  YES            1             34
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APCS MUTATED       0                         0    13
  APCS WILD-TYPE     5                         1   271
D98V13, multiclass
                           clus
vv                          APCS MUTATED APCS WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               13            271
[1] 3 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
  APCS MUTATED     0  13
  APCS WILD-TYPE   3 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  APCS MUTATED      0   13
  APCS WILD-TYPE    3  270
                        clus
vv                       APCS MUTATED APCS WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13            270
[1] 2 2
[1] FALSE

Clustering(99) Variable = GPX5 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2             0  1
  GPX5 MUTATED    6  4
  GPX5 WILD-TYPE 91 99
  GPX5 MUTATED GPX5 WILD-TYPE 
            10            190 
  GPX5 MUTATED GPX5 WILD-TYPE 
             4             99 
$`GPX5 MUTATED`
TCGA-EE-A20H TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A5GL TCGA-EB-A5UN TCGA-EE-A29D 
      166.75        19.04        36.85        42.05        52.41        12.99 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-FS-A1ZQ 
      124.31        54.51        45.90       130.95 

$`GPX5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24        31.96       269.03        52.90 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
      134.40        27.35         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       11.34        45.70       177.86        15.02        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
        3.91        16.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        0.26        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       63.25        89.26       104.78       145.45       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       23.51        53.26       122.73        64.04         4.41         6.28 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       67.89       111.85         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       49.74       195.98         8.35        27.62       312.07        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT 
       43.92         7.82        36.33        78.61       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  GPX5 MUTATED GPX5 WILD-TYPE 
         12.99           0.00 
  GPX5 MUTATED GPX5 WILD-TYPE 
        166.75         346.49 
  GPX5 MUTATED GPX5 WILD-TYPE 
        49.155         47.295 
[1] "13.0 - 166.8 (49.2)" "0.0 - 346.5 (47.3)" 
[1] "hr=" "1.2"
D99V2, survival
                sevent
clus2              0   1
  GPX5 MUTATED     9   8
  GPX5 WILD-TYPE 115 152
  GPX5 MUTATED GPX5 WILD-TYPE 
            17            267 
  GPX5 MUTATED GPX5 WILD-TYPE 
             8            152 
$`GPX5 MUTATED`
TCGA-EE-A20H TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU 
      168.26        31.40        36.95       125.79       137.92       125.19 
TCGA-EB-A5UN TCGA-EE-A29D TCGA-EE-A29S TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 
       58.92        13.97        61.28       124.31        54.51        64.08 
TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A4U9 
       23.93       133.55        28.73        15.78        22.13 

$`GPX5 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       18.18       151.53        54.67         3.65         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        29.29         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       66.74        14.47       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       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-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       64.04        28.77        13.81        41.59       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE 
      127.20        36.95        34.32        53.19       201.80        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
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        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        46.45         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-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        77.82        66.67       174.84        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        19.43         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
      121.91        39.35        10.42        48.89       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  GPX5 MUTATED GPX5 WILD-TYPE 
         13.97           0.20 
  GPX5 MUTATED GPX5 WILD-TYPE 
        168.26         369.93 
  GPX5 MUTATED GPX5 WILD-TYPE 
         58.92          53.52 
[1] "14.0 - 168.3 (58.9)" "0.2 - 369.9 (53.5)" 
[1] "hr=" "1.1"
D99V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  GPX5 MUTATED          2       0       2        1        3        2         1
  GPX5 WILD-TYPE        8       6      23        9       22       16         9
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GPX5 MUTATED           1         1         2          0          1          2
  GPX5 WILD-TYPE        13         9        34         14         25         41
                vv
clus             STAGE IV
  GPX5 MUTATED          0
  GPX5 WILD-TYPE       16
D99V4, multiclass
            clus
vv           GPX5 MUTATED GPX5 WILD-TYPE
  I/II NOS              2              8
  STAGE 0               0              6
  STAGE I               2             23
  STAGE IA              1              9
  STAGE IB              3             22
  STAGE II              2             16
  STAGE IIA             1              9
  STAGE IIB             1             13
  STAGE IIC             1              9
  STAGE III             2             34
  STAGE IIIA            0             14
  STAGE IIIB            1             25
  STAGE IIIC            2             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
  GPX5 MUTATED       3  6  3  3
  GPX5 WILD-TYPE    50 56 57 52
D99V5, multiclass
       clus
vv      GPX5 MUTATED GPX5 WILD-TYPE
  T0+T1            3             50
  T2               6             56
  T3               3             57
  T4               3             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GPX5 MUTATED    12   1   2   1
  GPX5 WILD-TYPE 131  52  32  34
D99V6, multiclass
    clus
vv   GPX5 MUTATED GPX5 WILD-TYPE
  N0           12            131
  N1            1             52
  N2            2             32
  N3            1             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"
D99V7, binary
                cls
clus               0   1
  GPX5 MUTATED    17   0
  GPX5 WILD-TYPE 239  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX5 MUTATED     17    0
  GPX5 WILD-TYPE  239   17
   clus
vv  GPX5 MUTATED GPX5 WILD-TYPE
  0           17            239
  1            0             17
[1] 2 2
[1] FALSE
D99V8, binary
                cls
clus               0   1
  GPX5 MUTATED     6   4
  GPX5 WILD-TYPE 101  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX5 MUTATED      6    4
  GPX5 WILD-TYPE  101   69
     clus
vv    GPX5 MUTATED GPX5 WILD-TYPE
  NO             6            101
  YES            4             69
[1] 2 2
[1] FALSE
D99V9, binary
                cls
clus               0   1
  GPX5 MUTATED     2  16
  GPX5 WILD-TYPE  35 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX5 MUTATED      2   16
  GPX5 WILD-TYPE   35  237
     clus
vv    GPX5 MUTATED GPX5 WILD-TYPE
  NO             2             35
  YES           16            237
[1] 2 2
[1] FALSE
D99V10, continuous
D99V11, binary
                cls
clus               0   1
  GPX5 MUTATED     3  15
  GPX5 WILD-TYPE 106 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX5 MUTATED      3   15
  GPX5 WILD-TYPE  106  166
        clus
vv       GPX5 MUTATED GPX5 WILD-TYPE
  FEMALE            3            106
  MALE             15            166
[1] 2 2
[1] FALSE
D99V12, binary
                cls
clus               0   1
  GPX5 MUTATED    15   3
  GPX5 WILD-TYPE 239  32
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX5 MUTATED     15    3
  GPX5 WILD-TYPE  239   32
     clus
vv    GPX5 MUTATED GPX5 WILD-TYPE
  NO            15            239
  YES            3             32
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPX5 MUTATED       0                         0    18
  GPX5 WILD-TYPE     5                         1   266
D99V13, multiclass
                           clus
vv                          GPX5 MUTATED GPX5 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               18            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"
D99V14, binary
                cls
clus               0   1
  GPX5 MUTATED     0  18
  GPX5 WILD-TYPE   3 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX5 MUTATED      0   18
  GPX5 WILD-TYPE    3  265
                        clus
vv                       GPX5 MUTATED GPX5 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           18            265
[1] 2 2
[1] FALSE

Clustering(100) Variable = PDK4 MUTATION ANALYSIS
D100V1, survival
                sevent
clus2              0   1
  PDK4 MUTATED     3   2
  PDK4 WILD-TYPE  94 101
  PDK4 MUTATED PDK4 WILD-TYPE 
             5            195 
  PDK4 MUTATED PDK4 WILD-TYPE 
             2            101 
$`PDK4 MUTATED`
TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-EE-A29E 
       36.85        62.86        22.29        22.85         0.26 

$`PDK4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        27.35        19.04         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       62.60        25.64        45.99        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       69.21        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       20.38         0.00        26.24        75.55        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       76.14        12.99        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      143.93        23.51        53.26       124.31       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
        4.41        54.51         6.28        67.89       111.85        45.90 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
        3.35       168.85        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  PDK4 MUTATED PDK4 WILD-TYPE 
          0.26           0.00 
  PDK4 MUTATED PDK4 WILD-TYPE 
         62.86         346.49 
  PDK4 MUTATED PDK4 WILD-TYPE 
         22.85          47.74 
[1] "0.3 - 62.9 (22.9)"  "0.0 - 346.5 (47.7)"
[1] "hr=" "1.7"
D100V2, survival
                sevent
clus2              0   1
  PDK4 MUTATED     3   4
  PDK4 WILD-TYPE 121 156
  PDK4 MUTATED PDK4 WILD-TYPE 
             7            277 
  PDK4 MUTATED PDK4 WILD-TYPE 
             4            156 
$`PDK4 MUTATED`
TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-EE-A29E TCGA-FS-A1ZA 
       36.95        65.49        22.29        22.95        63.78        27.72 
TCGA-GN-A266 
       10.13 

$`PDK4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       27.35        31.40        50.76        15.45        16.57        16.67 
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-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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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-A6E9 TCGA-D9-A6EA 
       54.67         3.65         7.10        15.39         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       77.56        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        85.08        78.97        13.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         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        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2.04        15.78       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  PDK4 MUTATED PDK4 WILD-TYPE 
         10.13           0.20 
  PDK4 MUTATED PDK4 WILD-TYPE 
         65.49         369.93 
  PDK4 MUTATED PDK4 WILD-TYPE 
         27.72          54.41 
[1] "10.1 - 65.5 (27.7)" "0.2 - 369.9 (54.4)"
[1] "hr=" "2"  
D100V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PDK4 MUTATED          0       0       0        0        1        0         0
  PDK4 WILD-TYPE       10       6      25       10       24       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PDK4 MUTATED           0         0         1          1          3          0
  PDK4 WILD-TYPE        14        10        35         13         23         43
                vv
clus             STAGE IV
  PDK4 MUTATED          0
  PDK4 WILD-TYPE       16
D100V4, multiclass
            clus
vv           PDK4 MUTATED PDK4 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               0             25
  STAGE IA              0             10
  STAGE IB              1             24
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             0             14
  STAGE IIC             0             10
  STAGE III             1             35
  STAGE IIIA            1             13
  STAGE IIIB            3             23
  STAGE IIIC            0             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
  PDK4 MUTATED       0  1  2  2
  PDK4 WILD-TYPE    53 61 58 53
D100V5, multiclass
       clus
vv      PDK4 MUTATED PDK4 WILD-TYPE
  T0+T1            0             53
  T2               1             61
  T3               2             58
  T4               2             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PDK4 MUTATED     1   3   2   0
  PDK4 WILD-TYPE 142  50  32  35
D100V6, multiclass
    clus
vv   PDK4 MUTATED PDK4 WILD-TYPE
  N0            1            142
  N1            3             50
  N2            2             32
  N3            0             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"
D100V7, binary
                cls
clus               0   1
  PDK4 MUTATED     6   0
  PDK4 WILD-TYPE 250  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK4 MUTATED      6    0
  PDK4 WILD-TYPE  250   17
   clus
vv  PDK4 MUTATED PDK4 WILD-TYPE
  0            6            250
  1            0             17
[1] 2 2
[1] FALSE
D100V8, binary
                cls
clus               0   1
  PDK4 MUTATED     3   2
  PDK4 WILD-TYPE 104  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK4 MUTATED      3    2
  PDK4 WILD-TYPE  104   71
     clus
vv    PDK4 MUTATED PDK4 WILD-TYPE
  NO             3            104
  YES            2             71
[1] 2 2
[1] FALSE
D100V9, binary
                cls
clus               0   1
  PDK4 MUTATED     1   6
  PDK4 WILD-TYPE  36 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK4 MUTATED      1    6
  PDK4 WILD-TYPE   36  247
     clus
vv    PDK4 MUTATED PDK4 WILD-TYPE
  NO             1             36
  YES            6            247
[1] 2 2
[1] FALSE
D100V10, continuous
D100V11, binary
                cls
clus               0   1
  PDK4 MUTATED     2   5
  PDK4 WILD-TYPE 107 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK4 MUTATED      2    5
  PDK4 WILD-TYPE  107  176
        clus
vv       PDK4 MUTATED PDK4 WILD-TYPE
  FEMALE            2            107
  MALE              5            176
[1] 2 2
[1] FALSE
D100V12, binary
                cls
clus               0   1
  PDK4 MUTATED     6   1
  PDK4 WILD-TYPE 248  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK4 MUTATED      6    1
  PDK4 WILD-TYPE  248   34
     clus
vv    PDK4 MUTATED PDK4 WILD-TYPE
  NO             6            248
  YES            1             34
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDK4 MUTATED       0                         0     7
  PDK4 WILD-TYPE     5                         1   277
D100V13, multiclass
                           clus
vv                          PDK4 MUTATED PDK4 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                7            277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V14, binary
                cls
clus               0   1
  PDK4 MUTATED     0   7
  PDK4 WILD-TYPE   3 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK4 MUTATED      0    7
  PDK4 WILD-TYPE    3  276
                        clus
vv                       PDK4 MUTATED PDK4 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            7            276
[1] 2 2
[1] FALSE

Clustering(101) Variable = EPS8 MUTATION ANALYSIS
D101V1, survival
                sevent
clus2             0  1
  EPS8 MUTATED    2  4
  EPS8 WILD-TYPE 95 99
  EPS8 MUTATED EPS8 WILD-TYPE 
             6            194 
  EPS8 MUTATED EPS8 WILD-TYPE 
             4             99 
$`EPS8 MUTATED`
TCGA-EE-A3JD TCGA-DA-A1I1 TCGA-EE-A29D TCGA-EE-A2A2 TCGA-ER-A19P TCGA-ER-A2NC 
       27.35        68.68        12.99        30.02       120.76        22.36 

$`EPS8 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       79.20        75.22        76.14         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84        42.51        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18       146.63        73.05         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  EPS8 MUTATED EPS8 WILD-TYPE 
         12.99           0.00 
  EPS8 MUTATED EPS8 WILD-TYPE 
        120.76         346.49 
  EPS8 MUTATED EPS8 WILD-TYPE 
        28.685         47.575 
[1] "13.0 - 120.8 (28.7)" "0.0 - 346.5 (47.6)" 
[1] "hr=" "1.8"
D101V2, survival
                sevent
clus2              0   1
  EPS8 MUTATED     2   5
  EPS8 WILD-TYPE 122 155
  EPS8 MUTATED EPS8 WILD-TYPE 
             7            277 
  EPS8 MUTATED EPS8 WILD-TYPE 
             5            155 
$`EPS8 MUTATED`
TCGA-EE-A184 TCGA-EE-A3JD TCGA-DA-A1I1 TCGA-EE-A29D TCGA-EE-A2A2 TCGA-ER-A19P 
       68.15        27.35       222.51        13.97        59.64       162.08 
TCGA-ER-A2NC 
       43.82 

$`EPS8 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 
      168.26         2.60       340.14       126.81       134.40        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        85.08        78.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64        56.84        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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-A2GE 
      115.96        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       50.89        49.48         8.88       148.18       105.07        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.78       139.89       117.93        96.92        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  EPS8 MUTATED EPS8 WILD-TYPE 
         13.97           0.20 
  EPS8 MUTATED EPS8 WILD-TYPE 
        222.51         369.93 
  EPS8 MUTATED EPS8 WILD-TYPE 
         59.64          53.92 
[1] "14.0 - 222.5 (59.6)" "0.2 - 369.9 (53.9)" 
[1] "hr=" "1.1"
D101V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  EPS8 MUTATED          0       0       0        0        2        0         0
  EPS8 WILD-TYPE       10       6      25       10       23       18        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EPS8 MUTATED           0         0         2          0          0          2
  EPS8 WILD-TYPE        14        10        34         14         26         41
                vv
clus             STAGE IV
  EPS8 MUTATED          0
  EPS8 WILD-TYPE       16
D101V4, multiclass
            clus
vv           EPS8 MUTATED EPS8 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               0              6
  STAGE I               0             25
  STAGE IA              0             10
  STAGE IB              2             23
  STAGE II              0             18
  STAGE IIA             0             10
  STAGE IIB             0             14
  STAGE IIC             0             10
  STAGE III             2             34
  STAGE IIIA            0             14
  STAGE IIIB            0             26
  STAGE IIIC            2             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
  EPS8 MUTATED       1  2  1  1
  EPS8 WILD-TYPE    52 60 59 54
D101V5, multiclass
       clus
vv      EPS8 MUTATED EPS8 WILD-TYPE
  T0+T1            1             52
  T2               2             60
  T3               1             59
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EPS8 MUTATED     3   2   2   0
  EPS8 WILD-TYPE 140  51  32  35
D101V6, multiclass
    clus
vv   EPS8 MUTATED EPS8 WILD-TYPE
  N0            3            140
  N1            2             51
  N2            2             32
  N3            0             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"
D101V7, binary
                cls
clus               0   1
  EPS8 MUTATED     7   0
  EPS8 WILD-TYPE 249  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      7    0
  EPS8 WILD-TYPE  249   17
   clus
vv  EPS8 MUTATED EPS8 WILD-TYPE
  0            7            249
  1            0             17
[1] 2 2
[1] FALSE
D101V8, binary
                cls
clus               0   1
  EPS8 MUTATED     2   2
  EPS8 WILD-TYPE 105  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      2    2
  EPS8 WILD-TYPE  105   71
     clus
vv    EPS8 MUTATED EPS8 WILD-TYPE
  NO             2            105
  YES            2             71
[1] 2 2
[1] FALSE
D101V9, binary
                cls
clus               0   1
  EPS8 MUTATED     2   5
  EPS8 WILD-TYPE  35 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      2    5
  EPS8 WILD-TYPE   35  248
     clus
vv    EPS8 MUTATED EPS8 WILD-TYPE
  NO             2             35
  YES            5            248
[1] 2 2
[1] FALSE
D101V10, continuous
D101V11, binary
                cls
clus               0   1
  EPS8 MUTATED     1   6
  EPS8 WILD-TYPE 108 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      1    6
  EPS8 WILD-TYPE  108  175
        clus
vv       EPS8 MUTATED EPS8 WILD-TYPE
  FEMALE            1            108
  MALE              6            175
[1] 2 2
[1] FALSE
D101V12, binary
                cls
clus               0   1
  EPS8 MUTATED     7   0
  EPS8 WILD-TYPE 247  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      7    0
  EPS8 WILD-TYPE  247   35
     clus
vv    EPS8 MUTATED EPS8 WILD-TYPE
  NO             7            247
  YES            0             35
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPS8 MUTATED       0                         0     7
  EPS8 WILD-TYPE     5                         1   277
D101V13, multiclass
                           clus
vv                          EPS8 MUTATED EPS8 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                7            277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V14, binary
                cls
clus               0   1
  EPS8 MUTATED     0   7
  EPS8 WILD-TYPE   3 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPS8 MUTATED      0    7
  EPS8 WILD-TYPE    3  276
                        clus
vv                       EPS8 MUTATED EPS8 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            7            276
[1] 2 2
[1] FALSE

Clustering(102) Variable = LUZP1 MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2               0   1
  LUZP1 MUTATED     2   3
  LUZP1 WILD-TYPE  95 100
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              5             195 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              3             100 
$`LUZP1 MUTATED`
TCGA-EE-A2MR TCGA-EE-A29B TCGA-EE-A2GB TCGA-FS-A1Z0 TCGA-FS-A1ZQ 
      134.40        75.22        26.14       195.98       130.95 

$`LUZP1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90        27.35        19.04        36.85         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       15.02        22.29        69.21        22.85        76.34       138.67 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN 
       30.44       225.11        42.64         3.91        16.41        52.41 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       18.21        13.15        24.89        20.38         0.00        26.24 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       75.55        79.20        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        30.02        77.98        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.82        36.33        78.61       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  LUZP1 MUTATED LUZP1 WILD-TYPE 
          26.14            0.00 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
         195.98          346.49 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
         130.95           46.92 
[1] "26.1 - 196.0 (130.9)" "0.0 - 346.5 (46.9)"  
[1] "hr=" "1.4"
D102V2, survival
                 sevent
clus2               0   1
  LUZP1 MUTATED     2   4
  LUZP1 WILD-TYPE 122 156
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              6             278 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              4             156 
$`LUZP1 MUTATED`
TCGA-EE-A2MR TCGA-EE-A29B TCGA-EE-A2GB TCGA-EE-A2MQ TCGA-FS-A1Z0 TCGA-FS-A1ZQ 
      134.40        85.08        59.28        43.23       202.65       133.55 

$`LUZP1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       126.81        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       31.40        50.76        15.45        36.95        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        77.56        22.95        76.57        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      144.89        20.38       222.51       176.55        35.93       135.02 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        78.97        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-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65       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 
       64.04        28.77        54.51        13.81        41.59       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-A195 TCGA-ER-A197 
      201.80        51.35       134.33       152.81        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       302.07       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 
       44.09       162.08        50.89        49.48         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      105.07        43.82        23.34        20.15        28.83        48.99 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       41.56       247.04        93.01        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
      149.03        92.98       174.21        15.72       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        15.78       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  LUZP1 MUTATED LUZP1 WILD-TYPE 
          43.23            0.20 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
         202.65          369.93 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
        109.315          53.390 
[1] "43.2 - 202.7 (109.3)" "0.2 - 369.9 (53.4)"  
[1] "hr=" "1.2"
D102V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  LUZP1 MUTATED          1       0       1        1        0        0         0
  LUZP1 WILD-TYPE        9       6      24        9       25       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LUZP1 MUTATED           1         0         0          1          1
  LUZP1 WILD-TYPE        13        10        36         13         25
                 vv
clus              STAGE IIIC STAGE IV
  LUZP1 MUTATED            0        0
  LUZP1 WILD-TYPE         43       16
D102V4, multiclass
            clus
vv           LUZP1 MUTATED LUZP1 WILD-TYPE
  I/II NOS               1               9
  STAGE 0                0               6
  STAGE I                1              24
  STAGE IA               1               9
  STAGE IB               0              25
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              1              13
  STAGE IIC              0              10
  STAGE III              0              36
  STAGE IIIA             1              13
  STAGE IIIB             1              25
  STAGE IIIC             0              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
  LUZP1 MUTATED       1  2  2  0
  LUZP1 WILD-TYPE    52 60 58 55
D102V5, multiclass
       clus
vv      LUZP1 MUTATED LUZP1 WILD-TYPE
  T0+T1             1              52
  T2                2              60
  T3                2              58
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LUZP1 MUTATED     4   1   1   0
  LUZP1 WILD-TYPE 139  52  33  35
D102V6, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  N0             4             139
  N1             1              52
  N2             1              33
  N3             0              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"
D102V7, binary
                 cls
clus                0   1
  LUZP1 MUTATED     6   0
  LUZP1 WILD-TYPE 250  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      6    0
  LUZP1 WILD-TYPE  250   17
   clus
vv  LUZP1 MUTATED LUZP1 WILD-TYPE
  0             6             250
  1             0              17
[1] 2 2
[1] FALSE
D102V8, binary
                 cls
clus                0   1
  LUZP1 MUTATED     3   2
  LUZP1 WILD-TYPE 104  71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      3    2
  LUZP1 WILD-TYPE  104   71
     clus
vv    LUZP1 MUTATED LUZP1 WILD-TYPE
  NO              3             104
  YES             2              71
[1] 2 2
[1] FALSE
D102V9, binary
                 cls
clus                0   1
  LUZP1 MUTATED     0   6
  LUZP1 WILD-TYPE  37 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      0    6
  LUZP1 WILD-TYPE   37  247
     clus
vv    LUZP1 MUTATED LUZP1 WILD-TYPE
  NO              0              37
  YES             6             247
[1] 2 2
[1] FALSE
D102V10, continuous
D102V11, binary
                 cls
clus                0   1
  LUZP1 MUTATED     2   4
  LUZP1 WILD-TYPE 107 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      2    4
  LUZP1 WILD-TYPE  107  177
        clus
vv       LUZP1 MUTATED LUZP1 WILD-TYPE
  FEMALE             2             107
  MALE               4             177
[1] 2 2
[1] FALSE
D102V12, binary
                 cls
clus                0   1
  LUZP1 MUTATED     3   3
  LUZP1 WILD-TYPE 251  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      3    3
  LUZP1 WILD-TYPE  251   32
     clus
vv    LUZP1 MUTATED LUZP1 WILD-TYPE
  NO              3             251
  YES             3              32
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LUZP1 MUTATED       0                         0     6
  LUZP1 WILD-TYPE     5                         1   278
D102V13, multiclass
                           clus
vv                          LUZP1 MUTATED LUZP1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 6             278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V14, binary
                 cls
clus                0   1
  LUZP1 MUTATED     0   6
  LUZP1 WILD-TYPE   3 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      0    6
  LUZP1 WILD-TYPE    3  277
                        clus
vv                       LUZP1 MUTATED LUZP1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             277
[1] 2 2
[1] FALSE

Clustering(103) Variable = C10ORF118 MUTATION ANALYSIS
D103V1, survival
                     sevent
clus2                   0   1
  C10ORF118 MUTATED     3   1
  C10ORF118 WILD-TYPE  94 102
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
                  4                 196 
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
                  1                 102 
$`C10ORF118 MUTATED`
TCGA-FW-A3R5 TCGA-D9-A6EC TCGA-EE-A29M TCGA-FS-A1Z3 
       36.85        69.21        47.74         8.35 

$`C10ORF118 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        27.35        19.04         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        22.29        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       34.45        10.49         7.82         4.54        53.29        39.81 
TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.47       184.60       150.12        99.06        59.84        42.51 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      120.76        49.71        47.18       146.63        73.05        22.36 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        4.70        16.87        10.19        28.67       173.29        68.52 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW 
       15.48        32.05        74.47         4.50       174.21       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       49.74       195.98        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
               8.35                0.00 
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
              69.21              346.49 
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
             42.295              47.295 
[1] "8.3 - 69.2 (42.3)"  "0.0 - 346.5 (47.3)"
[1] "hr=" "1.3"
D103V2, survival
                     sevent
clus2                   0   1
  C10ORF118 MUTATED     3   4
  C10ORF118 WILD-TYPE 121 156
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
                  7                 277 
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
                  4                 156 
$`C10ORF118 MUTATED`
TCGA-FW-A3R5 TCGA-D9-A6EC TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2MD TCGA-FS-A1Z3 
       36.95        77.56        56.84        18.61        47.28        20.91 
TCGA-GN-A266 
       10.13 

$`C10ORF118 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       27.35        31.40        50.76        15.45        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       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         7.10        15.39        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       222.51       176.55        35.93       135.02        88.87 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        40.60        68.09        33.93        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL 
      225.96        43.36        13.87        10.36        20.35        29.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       58.92         7.04        36.46        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        85.08        78.97        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       63.78        72.07        64.64        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       61.28       369.93        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 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48       102.12        13.91        42.77        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        46.45         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        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2.04        15.78       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       48.89        22.13       297.90         7.23         0.20         0.33 
TCGA-RP-A694 
        0.69 

  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
              10.13                0.20 
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
              77.56              369.93 
  C10ORF118 MUTATED C10ORF118 WILD-TYPE 
              36.95               54.41 
[1] "10.1 - 77.6 (37.0)" "0.2 - 369.9 (54.4)"
[1] "hr=" "1.9"
D103V3, continuous
                     vv
clus                  I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  C10ORF118 MUTATED          1       0       0        0        1        1
  C10ORF118 WILD-TYPE        9       6      25       10       24       17
                     vv
clus                  STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  C10ORF118 MUTATED           0         0         0         1          1
  C10ORF118 WILD-TYPE        10        14        10        35         13
                     vv
clus                  STAGE IIIB STAGE IIIC STAGE IV
  C10ORF118 MUTATED            0          0        1
  C10ORF118 WILD-TYPE         26         43       15
D103V4, multiclass
            clus
vv           C10ORF118 MUTATED C10ORF118 WILD-TYPE
  I/II NOS                   1                   9
  STAGE 0                    0                   6
  STAGE I                    0                  25
  STAGE IA                   0                  10
  STAGE IB                   1                  24
  STAGE II                   1                  17
  STAGE IIA                  0                  10
  STAGE IIB                  0                  14
  STAGE IIC                  0                  10
  STAGE III                  1                  35
  STAGE IIIA                 1                  13
  STAGE IIIB                 0                  26
  STAGE IIIC                 0                  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
  C10ORF118 MUTATED       0  1  2  0
  C10ORF118 WILD-TYPE    53 61 58 55
D103V5, multiclass
       clus
vv      C10ORF118 MUTATED C10ORF118 WILD-TYPE
  T0+T1                 0                  53
  T2                    1                  61
  T3                    2                  58
  T4                    0                  55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  C10ORF118 MUTATED     4   1   1   0
  C10ORF118 WILD-TYPE 139  52  33  35
D103V6, multiclass
    clus
vv   C10ORF118 MUTATED C10ORF118 WILD-TYPE
  N0                 4                 139
  N1                 1                  52
  N2                 1                  33
  N3                 0                  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"
D103V7, binary
                     cls
clus                    0   1
  C10ORF118 MUTATED     5   1
  C10ORF118 WILD-TYPE 251  16
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF118 MUTATED      5    1
  C10ORF118 WILD-TYPE  251   16
   clus
vv  C10ORF118 MUTATED C10ORF118 WILD-TYPE
  0                 5                 251
  1                 1                  16
[1] 2 2
[1] FALSE
D103V8, binary
                     cls
clus                    0   1
  C10ORF118 MUTATED     2   1
  C10ORF118 WILD-TYPE 105  72
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF118 MUTATED      2    1
  C10ORF118 WILD-TYPE  105   72
     clus
vv    C10ORF118 MUTATED C10ORF118 WILD-TYPE
  NO                  2                 105
  YES                 1                  72
[1] 2 2
[1] FALSE
D103V9, binary
                     cls
clus                    0   1
  C10ORF118 MUTATED     2   5
  C10ORF118 WILD-TYPE  35 248
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF118 MUTATED      2    5
  C10ORF118 WILD-TYPE   35  248
     clus
vv    C10ORF118 MUTATED C10ORF118 WILD-TYPE
  NO                  2                  35
  YES                 5                 248
[1] 2 2
[1] FALSE
D103V10, continuous
D103V11, binary
                     cls
clus                    0   1
  C10ORF118 MUTATED     2   5
  C10ORF118 WILD-TYPE 107 176
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF118 MUTATED      2    5
  C10ORF118 WILD-TYPE  107  176
        clus
vv       C10ORF118 MUTATED C10ORF118 WILD-TYPE
  FEMALE                 2                 107
  MALE                   5                 176
[1] 2 2
[1] FALSE
D103V12, binary
                     cls
clus                    0   1
  C10ORF118 MUTATED     6   1
  C10ORF118 WILD-TYPE 248  34
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF118 MUTATED      6    1
  C10ORF118 WILD-TYPE  248   34
     clus
vv    C10ORF118 MUTATED C10ORF118 WILD-TYPE
  NO                  6                 248
  YES                 1                  34
[1] 2 2
[1] FALSE
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C10ORF118 MUTATED       0                         0     7
  C10ORF118 WILD-TYPE     5                         1   277
D103V13, multiclass
                           clus
vv                          C10ORF118 MUTATED C10ORF118 WILD-TYPE
  ASIAN                                     0                   5
  BLACK OR AFRICAN AMERICAN                 0                   1
  WHITE                                     7                 277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V14, binary
                     cls
clus                    0   1
  C10ORF118 MUTATED     0   7
  C10ORF118 WILD-TYPE   3 276
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF118 MUTATED      0    7
  C10ORF118 WILD-TYPE    3  276
                        clus
vv                       C10ORF118 MUTATED C10ORF118 WILD-TYPE
  HISPANIC OR LATINO                     0                   3
  NOT HISPANIC OR LATINO                 7                 276
[1] 2 2
[1] FALSE

Clustering(104) Variable = OR51S1 MUTATION ANALYSIS
D104V1, survival
                  sevent
clus2               0  1
  OR51S1 MUTATED   12  8
  OR51S1 WILD-TYPE 85 95
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              20              180 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
               8               95 
$`OR51S1 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JO TCGA-D3-A3MR 
       38.76        52.90        27.35        36.85        66.08        90.21 
TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A183 TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GP 
      144.46        69.21        26.24        47.41        47.74         0.76 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3JI TCGA-ER-A19H 
       63.25        89.26       143.93        23.51       135.98       150.12 
TCGA-FS-A1Z3 TCGA-GN-A268 
        8.35        42.48 

$`OR51S1 WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2MR 
       62.07        33.24        31.96       166.75       269.03       134.40 
TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       19.04         8.42        15.72        31.89       110.93        49.35 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        64.83        43.53        58.06       140.98        40.01 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       59.70        24.53         9.34        23.67       173.85        30.67 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       31.76        62.70        11.34        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       15.02        22.29        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F 
       13.15        24.89        20.38         0.00        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29P 
       75.22        76.14        12.99         0.26        44.28        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       18.35        93.63         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      104.78       145.45       227.01        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35       168.85        19.86        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       99.06        59.84        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.50       174.21       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U3 
       53.29       117.93        96.92        17.06         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       34.49        46.92       297.01         7.23         0.20         0.33 

  OR51S1 MUTATED OR51S1 WILD-TYPE 
            0.76             0.00 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          150.12           346.49 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          50.320           46.455 
[1] "0.8 - 150.1 (50.3)" "0.0 - 346.5 (46.5)"
[1] "hr=" "1.2"
D104V2, survival
                  sevent
clus2                0   1
  OR51S1 MUTATED    17  13
  OR51S1 WILD-TYPE 107 147
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              30              254 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
              13              147 
$`OR51S1 MUTATED`
TCGA-D3-A3C8 TCGA-EE-A2GO TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A2JO TCGA-D3-A3C7 
       46.32       126.81        27.35        36.95        66.08        46.98 
TCGA-D3-A3MR TCGA-D3-A51J TCGA-D9-A6EC TCGA-EE-A183 TCGA-EE-A29H TCGA-EE-A29M 
      103.59       145.12        77.56        26.89        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MK 
       18.61        67.43        48.72        13.91        96.23       180.39 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19H 
      162.48        71.21        36.95        51.35       152.81       152.35 
TCGA-FS-A1Z3 TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A268 
       20.91        23.93        28.73        15.78        10.13        62.79 

$`OR51S1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 
      168.26         2.60       340.14       134.40        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-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-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       86.14        59.28       173.79       220.24       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       102.12        42.77        81.21        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-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MU 
      216.66       167.90        47.54       248.65        43.23        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       53.19       201.80       134.33        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-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      302.07         6.44       131.51        61.05        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        28.83        48.99        41.56       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       93.01        46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       46.45         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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        19.43         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        64.44        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  OR51S1 MUTATED OR51S1 WILD-TYPE 
           10.13             0.20 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          180.39           369.93 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
          54.095           53.970 
[1] "10.1 - 180.4 (54.1)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1.2"
D104V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  OR51S1 MUTATED          1       1       1        2        3        3
  OR51S1 WILD-TYPE        9       5      24        8       22       15
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  OR51S1 MUTATED           0         2         0         8          1
  OR51S1 WILD-TYPE        10        12        10        28         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  OR51S1 MUTATED            3          2        1
  OR51S1 WILD-TYPE         23         41       15
D104V4, multiclass
            clus
vv           OR51S1 MUTATED OR51S1 WILD-TYPE
  I/II NOS                1                9
  STAGE 0                 1                5
  STAGE I                 1               24
  STAGE IA                2                8
  STAGE IB                3               22
  STAGE II                3               15
  STAGE IIA               0               10
  STAGE IIB               2               12
  STAGE IIC               0               10
  STAGE III               8               28
  STAGE IIIA              1               13
  STAGE IIIB              3               23
  STAGE IIIC              2               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
  OR51S1 MUTATED       5  4  5  6
  OR51S1 WILD-TYPE    48 58 55 49
D104V5, multiclass
       clus
vv      OR51S1 MUTATED OR51S1 WILD-TYPE
  T0+T1              5               48
  T2                 4               58
  T3                 5               55
  T4                 6               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OR51S1 MUTATED    17   7   2   2
  OR51S1 WILD-TYPE 126  46  32  33
D104V6, multiclass
    clus
vv   OR51S1 MUTATED OR51S1 WILD-TYPE
  N0             17              126
  N1              7               46
  N2              2               32
  N3              2               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"
D104V7, binary
                  cls
clus                 0   1
  OR51S1 MUTATED    27   1
  OR51S1 WILD-TYPE 229  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     27    1
  OR51S1 WILD-TYPE  229   16
   clus
vv  OR51S1 MUTATED OR51S1 WILD-TYPE
  0             27              229
  1              1               16
[1] 2 2
[1] FALSE
D104V8, binary
                  cls
clus                0  1
  OR51S1 MUTATED   13  4
  OR51S1 WILD-TYPE 94 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     13    4
  OR51S1 WILD-TYPE   94   69
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  NO              13               94
  YES              4               69
[1] 2 2
[1] FALSE
D104V9, binary
                  cls
clus                 0   1
  OR51S1 MUTATED     7  23
  OR51S1 WILD-TYPE  30 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED      7   23
  OR51S1 WILD-TYPE   30  230
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  NO               7               30
  YES             23              230
[1] 2 2
[1] FALSE
D104V10, continuous
D104V11, binary
                  cls
clus                 0   1
  OR51S1 MUTATED    10  20
  OR51S1 WILD-TYPE  99 161
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     10   20
  OR51S1 WILD-TYPE   99  161
        clus
vv       OR51S1 MUTATED OR51S1 WILD-TYPE
  FEMALE             10               99
  MALE               20              161
[1] 2 2
[1] FALSE
D104V12, binary
                  cls
clus                 0   1
  OR51S1 MUTATED    24   6
  OR51S1 WILD-TYPE 230  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED     24    6
  OR51S1 WILD-TYPE  230   29
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  NO              24              230
  YES              6               29
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR51S1 MUTATED       0                         0    30
  OR51S1 WILD-TYPE     5                         1   254
D104V13, multiclass
                           clus
vv                          OR51S1 MUTATED OR51S1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 30              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"
D104V14, binary
                  cls
clus                 0   1
  OR51S1 MUTATED     0  30
  OR51S1 WILD-TYPE   3 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED      0   30
  OR51S1 WILD-TYPE    3  253
                        clus
vv                       OR51S1 MUTATED OR51S1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             30              253
[1] 2 2
[1] FALSE

Clustering(105) Variable = AMPD3 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2              0  1
  AMPD3 MUTATED    9  5
  AMPD3 WILD-TYPE 88 98
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             14             186 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
              5              98 
$`AMPD3 MUTATED`
TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A51E TCGA-DA-A1I5 
       19.04        36.85        66.08        43.53       173.85       110.53 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MM 
       12.99         0.26        68.65         0.20       103.13       145.45 
TCGA-EE-A3AA TCGA-GN-A4U4 
      124.31        34.49 

$`AMPD3 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90       134.40        27.35         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB 
      107.61        36.30       171.58        64.83        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       30.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       45.70       177.86        15.02        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       76.34       138.67        68.68       150.61        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
       26.24        75.55        79.20        75.22        76.14        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS 
       10.62        32.48        18.35        93.63         0.76        71.31 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
       81.99        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS 
      171.85        63.25        89.26       104.78       227.01       143.93 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.51        53.26       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      120.53        46.92       297.01         7.23         0.20         0.33 

  AMPD3 MUTATED AMPD3 WILD-TYPE 
            0.2             0.0 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
         173.85          346.49 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
         54.805          47.295 
[1] "0.2 - 173.8 (54.8)" "0.0 - 346.5 (47.3)"
[1] "hr=" "1.4"
D105V2, survival
                 sevent
clus2               0   1
  AMPD3 MUTATED    11  10
  AMPD3 WILD-TYPE 113 150
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             21             263 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
             10             150 
$`AMPD3 MUTATED`
TCGA-D3-A3ML TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A51E 
       13.87        31.40        36.95        66.08        59.57       174.84 
TCGA-DA-A1I5 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29S TCGA-EE-A2GJ TCGA-EE-A2GR 
      135.02        13.97        63.78        61.28       107.38        42.77 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MM TCGA-EE-A3AA TCGA-FS-A4FC 
       44.88       129.27        47.28       167.90       124.31        54.41 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A4U4 
       15.78        10.13        39.35 

$`AMPD3 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       62.07        46.32        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
      168.26         2.60       340.14       126.81       134.40        27.35 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.48       130.72        58.06        46.98       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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       88.87        53.92        65.92        40.60        68.09        33.93 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       225.96        43.36        13.87        10.36        20.35 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       29.29        58.92         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
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        66.74 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       14.47       369.93        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 
      115.96        59.64        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24        48.72        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
      102.12        13.91        81.21        94.82        21.67        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-A2MN TCGA-EE-A2MP 
      204.66        96.23       180.39       216.66        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       43.23       162.48        71.21        53.26       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FD 
       66.67        28.73       174.84        34.03        26.73        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48        48.00       121.91        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  AMPD3 MUTATED AMPD3 WILD-TYPE 
          10.13            0.20 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
         174.84          369.93 
  AMPD3 MUTATED AMPD3 WILD-TYPE 
          54.41           53.92 
[1] "10.1 - 174.8 (54.4)" "0.2 - 369.9 (53.9)" 
[1] "hr=" "1.1"
D105V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMPD3 MUTATED          2       0       2        1        0        2         4
  AMPD3 WILD-TYPE        8       6      23        9       25       16         6
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMPD3 MUTATED           1         0         2          1          2
  AMPD3 WILD-TYPE        13        10        34         13         24
                 vv
clus              STAGE IIIC STAGE IV
  AMPD3 MUTATED            3        1
  AMPD3 WILD-TYPE         40       15
D105V4, multiclass
            clus
vv           AMPD3 MUTATED AMPD3 WILD-TYPE
  I/II NOS               2               8
  STAGE 0                0               6
  STAGE I                2              23
  STAGE IA               1               9
  STAGE IB               0              25
  STAGE II               2              16
  STAGE IIA              4               6
  STAGE IIB              1              13
  STAGE IIC              0              10
  STAGE III              2              34
  STAGE IIIA             1              13
  STAGE IIIB             2              24
  STAGE IIIC             3              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
  AMPD3 MUTATED       5  4  8  1
  AMPD3 WILD-TYPE    48 58 52 54
D105V5, multiclass
       clus
vv      AMPD3 MUTATED AMPD3 WILD-TYPE
  T0+T1             5              48
  T2                4              58
  T3                8              52
  T4                1              54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AMPD3 MUTATED    12   2   3   2
  AMPD3 WILD-TYPE 131  51  31  33
D105V6, multiclass
    clus
vv   AMPD3 MUTATED AMPD3 WILD-TYPE
  N0            12             131
  N1             2              51
  N2             3              31
  N3             2              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"
D105V7, binary
                 cls
clus                0   1
  AMPD3 MUTATED    19   1
  AMPD3 WILD-TYPE 237  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED     19    1
  AMPD3 WILD-TYPE  237   16
   clus
vv  AMPD3 MUTATED AMPD3 WILD-TYPE
  0            19             237
  1             1              16
[1] 2 2
[1] FALSE
D105V8, binary
                 cls
clus               0  1
  AMPD3 MUTATED    9  4
  AMPD3 WILD-TYPE 98 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED      9    4
  AMPD3 WILD-TYPE   98   69
     clus
vv    AMPD3 MUTATED AMPD3 WILD-TYPE
  NO              9              98
  YES             4              69
[1] 2 2
[1] FALSE
D105V9, binary
                 cls
clus                0   1
  AMPD3 MUTATED     4  18
  AMPD3 WILD-TYPE  33 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED      4   18
  AMPD3 WILD-TYPE   33  235
     clus
vv    AMPD3 MUTATED AMPD3 WILD-TYPE
  NO              4              33
  YES            18             235
[1] 2 2
[1] FALSE
D105V10, continuous
D105V11, binary
                 cls
clus                0   1
  AMPD3 MUTATED     6  16
  AMPD3 WILD-TYPE 103 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED      6   16
  AMPD3 WILD-TYPE  103  165
        clus
vv       AMPD3 MUTATED AMPD3 WILD-TYPE
  FEMALE             6             103
  MALE              16             165
[1] 2 2
[1] FALSE
D105V12, binary
                 cls
clus                0   1
  AMPD3 MUTATED    19   3
  AMPD3 WILD-TYPE 235  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED     19    3
  AMPD3 WILD-TYPE  235   32
     clus
vv    AMPD3 MUTATED AMPD3 WILD-TYPE
  NO             19             235
  YES             3              32
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMPD3 MUTATED       0                         0    22
  AMPD3 WILD-TYPE     5                         1   262
D105V13, multiclass
                           clus
vv                          AMPD3 MUTATED AMPD3 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                22             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"
D105V14, binary
                 cls
clus                0   1
  AMPD3 MUTATED     0  22
  AMPD3 WILD-TYPE   3 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD3 MUTATED      0   22
  AMPD3 WILD-TYPE    3  261
                        clus
vv                       AMPD3 MUTATED AMPD3 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            22             261
[1] 2 2
[1] FALSE

Clustering(106) Variable = CD300E MUTATION ANALYSIS
D106V1, survival
                  sevent
clus2                0   1
  CD300E MUTATED     5   2
  CD300E WILD-TYPE  92 101
  CD300E MUTATED CD300E WILD-TYPE 
               7              193 
  CD300E MUTATED CD300E WILD-TYPE 
               2              101 
$`CD300E MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-DA-A1HV TCGA-EE-A2MT TCGA-EE-A3JB TCGA-ER-A19M 
       52.90       134.40        76.34        23.51       168.85        59.84 
TCGA-FS-A1Z3 
        8.35 

$`CD300E WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       27.35        19.04        36.85         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.29        69.21        22.85       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F 
       24.89        20.38         0.00        26.24        75.55        79.20 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       75.22        76.14        12.99         0.26        44.28        47.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.74        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01       143.93        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      150.12        99.06        42.51       120.76        49.71        47.18 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.50       174.21       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  CD300E MUTATED CD300E WILD-TYPE 
            8.35             0.00 
  CD300E MUTATED CD300E WILD-TYPE 
          168.85           346.49 
  CD300E MUTATED CD300E WILD-TYPE 
           59.84            46.92 
[1] "8.3 - 168.8 (59.8)" "0.0 - 346.5 (46.9)"
[1] "hr=" "1.9"
D106V2, survival
                  sevent
clus2                0   1
  CD300E MUTATED     6   4
  CD300E WILD-TYPE 118 156
  CD300E MUTATED CD300E WILD-TYPE 
              10              274 
  CD300E MUTATED CD300E WILD-TYPE 
               4              156 
$`CD300E MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-DA-A1HV TCGA-EE-A2MT TCGA-EE-A3AG TCGA-EE-A3JB 
      126.81       134.40        76.57        71.21        41.59       201.80 
TCGA-ER-A19M TCGA-FS-A1Z3 TCGA-FS-A1ZH TCGA-GF-A6C9 
       61.05        20.91        32.75        15.78 

$`CD300E WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A193 
       68.15       168.26         2.60       340.14        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        77.56        22.95        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65        43.23       162.48        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       64.04        28.77        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-A3JE 
      127.20        36.95        64.08        34.32        53.19        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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        46.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        19.43         2.04       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  CD300E MUTATED CD300E WILD-TYPE 
           15.78             0.20 
  CD300E MUTATED CD300E WILD-TYPE 
          201.80           369.93 
  CD300E MUTATED CD300E WILD-TYPE 
           66.13            53.72 
[1] "15.8 - 201.8 (66.1)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1.5"
D106V3, continuous
                  vv
clus               I/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      24       10       23       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  CD300E MUTATED           0         0         0         2          0
  CD300E WILD-TYPE        10        14        10        34         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  CD300E MUTATED            2          0        2
  CD300E WILD-TYPE         24         43       14
D106V4, multiclass
            clus
vv           CD300E MUTATED CD300E WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 1               24
  STAGE IA                0               10
  STAGE IB                2               23
  STAGE II                1               17
  STAGE IIA               0               10
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               2               34
  STAGE IIIA              0               14
  STAGE IIIB              2               24
  STAGE IIIC              0               43
  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    51 59 57 55
D106V5, multiclass
       clus
vv      CD300E MUTATED CD300E WILD-TYPE
  T0+T1              2               51
  T2                 3               59
  T3                 3               57
  T4                 0               55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CD300E MUTATED     5   1   3   0
  CD300E WILD-TYPE 138  52  31  35
D106V6, multiclass
    clus
vv   CD300E MUTATED CD300E WILD-TYPE
  N0              5              138
  N1              1               52
  N2              3               31
  N3              0               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"
D106V7, binary
                  cls
clus                 0   1
  CD300E MUTATED     7   2
  CD300E WILD-TYPE 249  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      7    2
  CD300E WILD-TYPE  249   15
   clus
vv  CD300E MUTATED CD300E WILD-TYPE
  0              7              249
  1              2               15
[1] 2 2
[1] FALSE
D106V8, binary
                  cls
clus                 0   1
  CD300E MUTATED     4   1
  CD300E WILD-TYPE 103  72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      4    1
  CD300E WILD-TYPE  103   72
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               4              103
  YES              1               72
[1] 2 2
[1] FALSE
D106V9, binary
                  cls
clus                 0   1
  CD300E MUTATED     4   6
  CD300E WILD-TYPE  33 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      4    6
  CD300E WILD-TYPE   33  247
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               4               33
  YES              6              247
[1] 2 2
[1] FALSE
D106V10, continuous
D106V11, binary
                  cls
clus                 0   1
  CD300E MUTATED     5   5
  CD300E WILD-TYPE 104 176
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      5    5
  CD300E WILD-TYPE  104  176
        clus
vv       CD300E MUTATED CD300E WILD-TYPE
  FEMALE              5              104
  MALE                5              176
[1] 2 2
[1] FALSE
D106V12, binary
                  cls
clus                 0   1
  CD300E MUTATED     7   3
  CD300E WILD-TYPE 247  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      7    3
  CD300E WILD-TYPE  247   32
     clus
vv    CD300E MUTATED CD300E WILD-TYPE
  NO               7              247
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD300E MUTATED       0                         0    10
  CD300E WILD-TYPE     5                         1   274
D106V13, multiclass
                           clus
vv                          CD300E MUTATED CD300E WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 10              274
[1] 3 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
  CD300E MUTATED     0  10
  CD300E WILD-TYPE   3 273
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD300E MUTATED      0   10
  CD300E WILD-TYPE    3  273
                        clus
vv                       CD300E MUTATED CD300E WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              273
[1] 2 2
[1] FALSE

Clustering(107) Variable = SAG MUTATION ANALYSIS
D107V1, survival
               sevent
clus2             0   1
  SAG MUTATED     3   2
  SAG WILD-TYPE  94 101
  SAG MUTATED SAG WILD-TYPE 
            5           195 
  SAG MUTATED SAG WILD-TYPE 
            2           101 
$`SAG MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A29M TCGA-EE-A2MC TCGA-FS-A1ZZ 
       52.90       134.40        47.74        23.77         3.06 

$`SAG WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       27.35        19.04        36.85         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 
       47.41        27.16        61.12       346.49       185.19       115.43 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       30.02        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MF 
       71.31        81.99       103.13        15.25         5.75       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X 
       42.48         7.59       120.53        34.49        46.92       297.01 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
        7.23         0.20         0.33 

  SAG MUTATED SAG WILD-TYPE 
         3.06          0.00 
  SAG MUTATED SAG WILD-TYPE 
       134.40        346.49 
  SAG MUTATED SAG WILD-TYPE 
        47.74         47.18 
[1] "3.1 - 134.4 (47.7)" "0.0 - 346.5 (47.2)"
[1] "hr=" "1.1"
D107V2, survival
               sevent
clus2             0   1
  SAG MUTATED     5   4
  SAG WILD-TYPE 119 156
  SAG MUTATED SAG WILD-TYPE 
            9           275 
  SAG MUTATED SAG WILD-TYPE 
            4           156 
$`SAG MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-D9-A6EA TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2GI 
      126.81       134.40        25.18        56.84        25.87        48.72 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-FS-A1ZZ 
       21.67        61.51        27.02 

$`SAG WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A3JD TCGA-ER-A193 
       68.15       168.26         2.60       340.14        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       50.76        15.45        36.95        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        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-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       77.56        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      222.51       176.55        35.93       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        18.61        56.42        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       61.28       369.93       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      220.24       107.38        54.74        79.66        75.48       102.12 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        42.77        81.21        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       28.83        19.76        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       180.39       216.66       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        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       41.59       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       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  SAG MUTATED SAG WILD-TYPE 
        21.67          0.20 
  SAG MUTATED SAG WILD-TYPE 
       134.40        369.93 
  SAG MUTATED SAG WILD-TYPE 
        48.72         54.02 
[1] "21.7 - 134.4 (48.7)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1"  
D107V3, continuous
               vv
clus            I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SAG MUTATED          1       1       3        1        1        1         0
  SAG WILD-TYPE        9       5      22        9       24       17        10
               vv
clus            STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SAG MUTATED           1         0         0          0          0          2
  SAG WILD-TYPE        13        10        36         14         26         41
               vv
clus            STAGE IV
  SAG MUTATED          0
  SAG WILD-TYPE       16
D107V4, multiclass
            clus
vv           SAG MUTATED SAG WILD-TYPE
  I/II NOS             1             9
  STAGE 0              1             5
  STAGE I              3            22
  STAGE IA             1             9
  STAGE IB             1            24
  STAGE II             1            17
  STAGE IIA            0            10
  STAGE IIB            1            13
  STAGE IIC            0            10
  STAGE III            0            36
  STAGE IIIA           0            14
  STAGE IIIB           0            26
  STAGE IIIC           2            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
  SAG MUTATED       1  4  3  1
  SAG WILD-TYPE    52 58 57 54
D107V5, multiclass
       clus
vv      SAG MUTATED SAG WILD-TYPE
  T0+T1           1            52
  T2              4            58
  T3              3            57
  T4              1            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  SAG MUTATED     9   1   0   1
  SAG WILD-TYPE 134  52  34  34
D107V6, multiclass
    clus
vv   SAG MUTATED SAG WILD-TYPE
  N0           9           134
  N1           1            52
  N2           0            34
  N3           1            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"
D107V7, binary
               cls
clus              0   1
  SAG MUTATED    11   0
  SAG WILD-TYPE 245  17
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED     11    0
  SAG WILD-TYPE  245   17
   clus
vv  SAG MUTATED SAG WILD-TYPE
  0          11           245
  1           0            17
[1] 2 2
[1] FALSE
D107V8, binary
               cls
clus              0   1
  SAG MUTATED     7   2
  SAG WILD-TYPE 100  71
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      7    2
  SAG WILD-TYPE  100   71
     clus
vv    SAG MUTATED SAG WILD-TYPE
  NO            7           100
  YES           2            71
[1] 2 2
[1] FALSE
D107V9, binary
               cls
clus              0   1
  SAG MUTATED     0  11
  SAG WILD-TYPE  37 242
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      0   11
  SAG WILD-TYPE   37  242
     clus
vv    SAG MUTATED SAG WILD-TYPE
  NO            0            37
  YES          11           242
[1] 2 2
[1] FALSE
D107V10, continuous
D107V11, binary
               cls
clus              0   1
  SAG MUTATED     3   8
  SAG WILD-TYPE 106 173
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      3    8
  SAG WILD-TYPE  106  173
        clus
vv       SAG MUTATED SAG WILD-TYPE
  FEMALE           3           106
  MALE             8           173
[1] 2 2
[1] FALSE
D107V12, binary
               cls
clus              0   1
  SAG MUTATED     8   3
  SAG WILD-TYPE 246  32
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      8    3
  SAG WILD-TYPE  246   32
     clus
vv    SAG MUTATED SAG WILD-TYPE
  NO            8           246
  YES           3            32
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SAG MUTATED       0                         0    11
  SAG WILD-TYPE     5                         1   273
D107V13, multiclass
                           clus
vv                          SAG MUTATED SAG WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                              11           273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V14, binary
               cls
clus              0   1
  SAG MUTATED     1  10
  SAG WILD-TYPE   2 273
[1] "tbl2"
               cls
clus            [,1] [,2]
  SAG MUTATED      1   10
  SAG WILD-TYPE    2  273
                        clus
vv                       SAG MUTATED SAG WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          10           273
[1] 2 2
[1] FALSE

Clustering(108) Variable = DDX17 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     3   1
  DDX17 WILD-TYPE  94 102
  DDX17 MUTATED DDX17 WILD-TYPE 
              4             196 
  DDX17 MUTATED DDX17 WILD-TYPE 
              1             102 
$`DDX17 MUTATED`
TCGA-FW-A3R5 TCGA-D3-A5GR TCGA-EE-A2A2 TCGA-ER-A195 
       36.85       177.86        30.02        34.45 

$`DDX17 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       52.90       134.40        27.35        19.04         8.42        15.72 
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       31.89       110.93        49.35       133.25        19.04        76.41 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       62.60        25.64        45.99        62.86        15.75       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       86.30       107.61        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       43.53        58.06       140.98        40.01        59.70        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
        9.34        90.21        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A3Z1 
       31.76        62.70        11.34        42.05        45.70        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
       22.29        69.21        22.85        76.34       138.67        68.68 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 
      150.61       110.53        60.10        64.83        58.85        30.44 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
      225.11        42.64         3.91        16.41        52.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C 
       13.15        24.89        20.38         0.00        26.24        75.55 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       79.20        75.22        76.14        12.99         0.26        44.28 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       47.41        47.74        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      115.43        77.98        26.14        12.95       201.60        68.65 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       10.62        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       71.31        81.99       103.13        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      209.79        94.19       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45       227.01       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 
      122.73        64.04         4.41        54.51         6.28        67.89 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
      111.85        45.90         3.35       168.85        19.86       135.98 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        4.47        23.21         5.29         3.06        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
      173.19        13.28        80.68        55.59        11.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        18.25         1.91        53.29       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
      297.01         7.23         0.20         0.33 

  DDX17 MUTATED DDX17 WILD-TYPE 
          30.02            0.00 
  DDX17 MUTATED DDX17 WILD-TYPE 
         177.86          346.49 
  DDX17 MUTATED DDX17 WILD-TYPE 
         35.650          47.575 
[1] "30.0 - 177.9 (35.7)" "0.0 - 346.5 (47.6)" 
[1] "hr=" "2.3"
D108V2, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     4   4
  DDX17 WILD-TYPE 120 156
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             276 
  DDX17 MUTATED DDX17 WILD-TYPE 
              4             156 
$`DDX17 MUTATED`
TCGA-FW-A3R5 TCGA-D3-A5GR TCGA-DA-A1I4 TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-ER-A195 
       36.95       178.32        35.93        59.64        48.72        35.44 
TCGA-ER-A19F TCGA-FS-A1ZA 
       26.37        27.72 

$`DDX17 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 
       27.35        31.40        50.76        15.45        16.57        16.67 
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-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        66.48        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98       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-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      125.79       135.75       137.92        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         7.10        15.39        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        77.56        22.95        76.57        36.03       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       222.51       176.55       135.02        88.87        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        40.60        68.09        33.93        10.49       225.96 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       43.36        13.87        10.36        20.35        29.29        58.92 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        7.04        36.46        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        85.08        78.97        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        66.74 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        61.28       369.93        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       115.96        39.29        86.14        59.28        67.43 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      173.79       220.24       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A197 TCGA-ER-A199 TCGA-ER-A19A 
       51.35       134.33       152.81        13.94         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       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       13.51        19.30         9.90        19.43         2.04        15.78 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        96.92        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 
       32.48        48.00       121.91        39.35        10.42        48.89 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  DDX17 MUTATED DDX17 WILD-TYPE 
          26.37            0.20 
  DDX17 MUTATED DDX17 WILD-TYPE 
         178.32          369.93 
  DDX17 MUTATED DDX17 WILD-TYPE 
          36.44           54.46 
[1] "26.4 - 178.3 (36.4)" "0.2 - 369.9 (54.5)" 
[1] "hr=" "1.1"
D108V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DDX17 MUTATED          0       0       0        1        0        0         0
  DDX17 WILD-TYPE       10       6      25        9       25       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DDX17 MUTATED           0         0         2          0          1
  DDX17 WILD-TYPE        14        10        34         14         25
                 vv
clus              STAGE IIIC STAGE IV
  DDX17 MUTATED            2        0
  DDX17 WILD-TYPE         41       16
D108V4, multiclass
            clus
vv           DDX17 MUTATED DDX17 WILD-TYPE
  I/II NOS               0              10
  STAGE 0                0               6
  STAGE I                0              25
  STAGE IA               1               9
  STAGE IB               0              25
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              2              34
  STAGE IIIA             0              14
  STAGE IIIB             1              25
  STAGE IIIC             2              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
  DDX17 MUTATED       2  0  1  2
  DDX17 WILD-TYPE    51 62 59 53
D108V5, multiclass
       clus
vv      DDX17 MUTATED DDX17 WILD-TYPE
  T0+T1             2              51
  T2                0              62
  T3                1              59
  T4                2              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDX17 MUTATED     3   2   3   0
  DDX17 WILD-TYPE 140  51  31  35
D108V6, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             3             140
  N1             2              51
  N2             3              31
  N3             0              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"
D108V7, binary
                 cls
clus                0   1
  DDX17 MUTATED     8   0
  DDX17 WILD-TYPE 248  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      8    0
  DDX17 WILD-TYPE  248   17
   clus
vv  DDX17 MUTATED DDX17 WILD-TYPE
  0             8             248
  1             0              17
[1] 2 2
[1] FALSE
D108V8, binary
                 cls
clus                0   1
  DDX17 MUTATED     1   3
  DDX17 WILD-TYPE 106  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      1    3
  DDX17 WILD-TYPE  106   70
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              1             106
  YES             3              70
[1] 2 2
[1] FALSE
D108V9, binary
                 cls
clus                0   1
  DDX17 MUTATED     0   8
  DDX17 WILD-TYPE  37 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      0    8
  DDX17 WILD-TYPE   37  245
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              0              37
  YES             8             245
[1] 2 2
[1] FALSE
D108V10, continuous
D108V11, binary
                 cls
clus                0   1
  DDX17 MUTATED     2   6
  DDX17 WILD-TYPE 107 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      2    6
  DDX17 WILD-TYPE  107  175
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             2             107
  MALE               6             175
[1] 2 2
[1] FALSE
D108V12, binary
                 cls
clus                0   1
  DDX17 MUTATED     8   0
  DDX17 WILD-TYPE 246  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      8    0
  DDX17 WILD-TYPE  246   35
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              8             246
  YES             0              35
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX17 MUTATED       0                         0     8
  DDX17 WILD-TYPE     5                         1   276
D108V13, multiclass
                           clus
vv                          DDX17 MUTATED DDX17 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 8             276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V14, binary
                 cls
clus                0   1
  DDX17 MUTATED     0   8
  DDX17 WILD-TYPE   3 275
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      0    8
  DDX17 WILD-TYPE    3  275
                        clus
vv                       DDX17 MUTATED DDX17 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             275
[1] 2 2
[1] FALSE

Clustering(109) Variable = RUFY4 MUTATION ANALYSIS
D109V1, survival
                 sevent
clus2               0   1
  RUFY4 MUTATED     7   2
  RUFY4 WILD-TYPE  90 101
  RUFY4 MUTATED RUFY4 WILD-TYPE 
              9             191 
  RUFY4 MUTATED RUFY4 WILD-TYPE 
              2             101 
$`RUFY4 MUTATED`
TCGA-EE-A180 TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-DA-A1I7 TCGA-EB-A5UN TCGA-EE-A29H 
       31.96       134.40        36.85        60.10        52.41        47.41 
TCGA-EE-A2MS TCGA-FS-A1ZC TCGA-RP-A693 
      143.93       312.07         0.33 

$`RUFY4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        38.76        33.24       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       27.35        19.04         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       69.21        22.85        76.34       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
      110.53        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
        3.91        16.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       12.99         0.26        44.28        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
      346.49       185.19       115.43        30.02        77.98        26.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       12.95       201.60        68.65        10.62        32.48        18.35 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       93.63         0.76         0.20        71.31        81.99       103.13 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       15.25         5.75        23.77       209.79        94.19       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       227.01        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      136.27        35.28         4.47        23.21         5.29         3.06 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
       18.51        66.67       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      117.93        96.92        17.06        42.48         7.59       120.53 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       34.49        46.92       297.01         7.23         0.20 

  RUFY4 MUTATED RUFY4 WILD-TYPE 
           0.33            0.00 
  RUFY4 MUTATED RUFY4 WILD-TYPE 
         312.07          346.49 
  RUFY4 MUTATED RUFY4 WILD-TYPE 
          52.41           46.92 
[1] "0.3 - 312.1 (52.4)" "0.0 - 346.5 (46.9)"
[1] "hr=" "3.6"
D109V2, survival
                 sevent
clus2               0   1
  RUFY4 MUTATED     8   3
  RUFY4 WILD-TYPE 116 157
  RUFY4 MUTATED RUFY4 WILD-TYPE 
             11             273 
  RUFY4 MUTATED RUFY4 WILD-TYPE 
              3             157 
$`RUFY4 MUTATED`
TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A5GS TCGA-DA-A1I7 
       94.98         2.60       134.40        36.95        18.18        88.87 
TCGA-EB-A5UN TCGA-EE-A29H TCGA-EE-A2MS TCGA-FS-A1ZC TCGA-RP-A693 
       58.92        64.64       162.48       357.37         0.33 

$`RUFY4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A184 
       62.07        46.32        13.87        68.25        54.02        68.15 
TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 
      168.26       340.14       126.81        27.35        31.40        50.76 
TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       15.45        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      178.32       125.19       151.53        54.67         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       135.02        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       20.35        29.29         7.04        36.46        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        14.70        26.89         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        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.97        63.78        72.07        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       59.28        67.43       173.79       220.24        48.72       107.38 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48       102.12        13.91        42.77 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       81.21        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       180.39       216.66       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23        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        64.04        28.77        54.51        13.81        41.59 
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-A195 
       53.19       201.80        51.35       134.33       152.81        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       302.07       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        44.09       162.08        50.89        49.48         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18       105.07        43.82        23.34        20.15        28.83 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       48.99        41.56       247.04        93.01        46.98        33.21 
TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW 
       12.95       149.03        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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72        48.85        53.52        46.45         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        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90        19.43         2.04        15.78       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       96.92        10.13        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A694 
        7.23         0.20         0.69 

  RUFY4 MUTATED RUFY4 WILD-TYPE 
           0.33            0.20 
  RUFY4 MUTATED RUFY4 WILD-TYPE 
         357.37          369.93 
  RUFY4 MUTATED RUFY4 WILD-TYPE 
          64.64           53.52 
[1] "0.3 - 357.4 (64.6)" "0.2 - 369.9 (53.5)"
[1] "hr=" "2.9"
D109V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  RUFY4 MUTATED          1       0       1        1        0        1         0
  RUFY4 WILD-TYPE        9       6      24        9       25       17        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RUFY4 MUTATED           0         1         2          0          1
  RUFY4 WILD-TYPE        14         9        34         14         25
                 vv
clus              STAGE IIIC STAGE IV
  RUFY4 MUTATED            1        2
  RUFY4 WILD-TYPE         42       14
D109V4, multiclass
            clus
vv           RUFY4 MUTATED RUFY4 WILD-TYPE
  I/II NOS               1               9
  STAGE 0                0               6
  STAGE I                1              24
  STAGE IA               1               9
  STAGE IB               0              25
  STAGE II               1              17
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              1               9
  STAGE III              2              34
  STAGE IIIA             0              14
  STAGE IIIB             1              25
  STAGE IIIC             1              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
  RUFY4 MUTATED       3  1  1  3
  RUFY4 WILD-TYPE    50 61 59 52
D109V5, multiclass
       clus
vv      RUFY4 MUTATED RUFY4 WILD-TYPE
  T0+T1             3              50
  T2                1              61
  T3                1              59
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RUFY4 MUTATED     5   1   2   1
  RUFY4 WILD-TYPE 138  52  32  34
D109V6, multiclass
    clus
vv   RUFY4 MUTATED RUFY4 WILD-TYPE
  N0             5             138
  N1             1              52
  N2             2              32
  N3             1              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"
D109V7, binary
                 cls
clus                0   1
  RUFY4 MUTATED     9   2
  RUFY4 WILD-TYPE 247  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY4 MUTATED      9    2
  RUFY4 WILD-TYPE  247   15
   clus
vv  RUFY4 MUTATED RUFY4 WILD-TYPE
  0             9             247
  1             2              15
[1] 2 2
[1] FALSE
D109V8, binary
                 cls
clus                0   1
  RUFY4 MUTATED     5   2
  RUFY4 WILD-TYPE 102  71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY4 MUTATED      5    2
  RUFY4 WILD-TYPE  102   71
     clus
vv    RUFY4 MUTATED RUFY4 WILD-TYPE
  NO              5             102
  YES             2              71
[1] 2 2
[1] FALSE
D109V9, binary
                 cls
clus                0   1
  RUFY4 MUTATED     2   9
  RUFY4 WILD-TYPE  35 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY4 MUTATED      2    9
  RUFY4 WILD-TYPE   35  244
     clus
vv    RUFY4 MUTATED RUFY4 WILD-TYPE
  NO              2              35
  YES             9             244
[1] 2 2
[1] FALSE
D109V10, continuous
D109V11, binary
                 cls
clus                0   1
  RUFY4 MUTATED     1  10
  RUFY4 WILD-TYPE 108 171
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY4 MUTATED      1   10
  RUFY4 WILD-TYPE  108  171
        clus
vv       RUFY4 MUTATED RUFY4 WILD-TYPE
  FEMALE             1             108
  MALE              10             171
[1] 2 2
[1] FALSE
D109V12, binary
                 cls
clus                0   1
  RUFY4 MUTATED    10   1
  RUFY4 WILD-TYPE 244  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY4 MUTATED     10    1
  RUFY4 WILD-TYPE  244   34
     clus
vv    RUFY4 MUTATED RUFY4 WILD-TYPE
  NO             10             244
  YES             1              34
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUFY4 MUTATED       0                         0    11
  RUFY4 WILD-TYPE     5                         1   273
D109V13, multiclass
                           clus
vv                          RUFY4 MUTATED RUFY4 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                11             273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V14, binary
                 cls
clus                0   1
  RUFY4 MUTATED     0  11
  RUFY4 WILD-TYPE   3 272
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY4 MUTATED      0   11
  RUFY4 WILD-TYPE    3  272
                        clus
vv                       RUFY4 MUTATED RUFY4 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            11             272
[1] 2 2
[1] FALSE

Clustering(110) Variable = MAP3K5 MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2               0  1
  MAP3K5 MUTATED    7  6
  MAP3K5 WILD-TYPE 90 97
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              13              187 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
               6               97 
$`MAP3K5 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q6 TCGA-D3-A51J TCGA-EE-A29E 
       62.07       134.40        19.04        49.35       144.46         0.26 
TCGA-EE-A2A2 TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AA TCGA-ER-A19M TCGA-ER-A42L 
       30.02       171.85        63.25       124.31        59.84        74.47 
TCGA-FS-A1Z3 
        8.35 

$`MAP3K5 WILD-TYPE`
TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       38.76        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       27.35        36.85         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      173.85        30.67        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       45.70       177.86        15.02        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       12.99        44.28        47.41        47.74        27.16        61.12 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      346.49       185.19       115.43        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2ML 
        5.75        23.77       209.79        94.19        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      145.45       227.01       143.93        23.51        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      184.60       150.12        99.06        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        4.50       174.21       171.78        49.74       195.98        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      312.07        32.78        43.92         7.82        36.33        78.61 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      130.95       136.27        35.28         4.47        23.21         5.29 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
        3.06        18.51        66.67       173.19        13.28        80.68 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        11.54        19.30         9.90        18.25         1.91 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
      120.53        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
            0.26             0.00 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
          171.85           346.49 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           62.07            45.99 
[1] "0.3 - 171.8 (62.1)" "0.0 - 346.5 (46.0)"
[1] "hr=" "1.1"
D110V2, survival
                  sevent
clus2                0   1
  MAP3K5 MUTATED     9   9
  MAP3K5 WILD-TYPE 115 151
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
              18              266 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
               9              151 
$`MAP3K5 MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q6 TCGA-D3-A51J TCGA-EE-A29E 
       62.07       134.40        31.40        71.80       145.12        63.78 
TCGA-EE-A2A2 TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-ER-A19M 
       59.64       204.66        96.23       124.31        36.95        61.05 
TCGA-ER-A2NH TCGA-ER-A42L TCGA-FS-A1Z3 TCGA-FS-A4F5 TCGA-GF-A6C9 TCGA-GN-A266 
       41.56       149.03        20.91        28.73        15.78        10.13 

$`MAP3K5 WILD-TYPE`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 
       46.32        13.87        68.25        54.02        94.98        68.15 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A198 
      168.26         2.60       340.14       126.81        27.35        50.76 
TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       15.45        36.95        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       15.39        22.29         9.90        25.18        77.56        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       76.57        36.03       144.89        20.38       222.51       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       135.02        88.87        53.92        65.92        40.60 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
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-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       85.08        78.97        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-A29T 
       18.61        56.42        66.74        14.47        61.28       369.93 
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       115.96        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66       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-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       64.04        28.77        54.51        13.81        41.59       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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        44.09       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        49.48         8.88       148.18       105.07        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        28.83        48.99       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21        12.95        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-A1ZG 
       27.72        48.85       357.37        53.52        46.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       174.84        34.03        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       54.41        80.68        17.46        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90        19.43         2.04       139.89       117.93        96.92 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           10.13             0.20 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
          204.66           369.93 
  MAP3K5 MUTATED MAP3K5 WILD-TYPE 
           61.56            53.39 
[1] "10.1 - 204.7 (61.6)" "0.2 - 369.9 (53.4)" 
[1] "hr=" "1.1"
D110V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  MAP3K5 MUTATED          0       1       1        1        2        1
  MAP3K5 WILD-TYPE       10       5      24        9       23       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  MAP3K5 MUTATED           0         2         0         5          0
  MAP3K5 WILD-TYPE        10        12        10        31         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  MAP3K5 MUTATED            2          2        2
  MAP3K5 WILD-TYPE         24         41       14
D110V4, multiclass
            clus
vv           MAP3K5 MUTATED MAP3K5 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 1                5
  STAGE I                 1               24
  STAGE IA                1                9
  STAGE IB                2               23
  STAGE II                1               17
  STAGE IIA               0               10
  STAGE IIB               2               12
  STAGE IIC               0               10
  STAGE III               5               31
  STAGE IIIA              0               14
  STAGE IIIB              2               24
  STAGE IIIC              2               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
  MAP3K5 MUTATED       3  3  4  5
  MAP3K5 WILD-TYPE    50 59 56 50
D110V5, multiclass
       clus
vv      MAP3K5 MUTATED MAP3K5 WILD-TYPE
  T0+T1              3               50
  T2                 3               59
  T3                 4               56
  T4                 5               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP3K5 MUTATED    10   5   1   1
  MAP3K5 WILD-TYPE 133  48  33  34
D110V6, multiclass
    clus
vv   MAP3K5 MUTATED MAP3K5 WILD-TYPE
  N0             10              133
  N1              5               48
  N2              1               33
  N3              1               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"
D110V7, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED    16   2
  MAP3K5 WILD-TYPE 240  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED     16    2
  MAP3K5 WILD-TYPE  240   15
   clus
vv  MAP3K5 MUTATED MAP3K5 WILD-TYPE
  0             16              240
  1              2               15
[1] 2 2
[1] FALSE
D110V8, binary
                  cls
clus                0  1
  MAP3K5 MUTATED   10  1
  MAP3K5 WILD-TYPE 97 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED     10    1
  MAP3K5 WILD-TYPE   97   72
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  NO              10               97
  YES              1               72
[1] 2 2
[1] FALSE
D110V9, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     5  15
  MAP3K5 WILD-TYPE  32 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      5   15
  MAP3K5 WILD-TYPE   32  238
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  NO               5               32
  YES             15              238
[1] 2 2
[1] FALSE
D110V10, continuous
D110V11, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     2  18
  MAP3K5 WILD-TYPE 107 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      2   18
  MAP3K5 WILD-TYPE  107  163
        clus
vv       MAP3K5 MUTATED MAP3K5 WILD-TYPE
  FEMALE              2              107
  MALE               18              163
[1] 2 2
[1] FALSE
D110V12, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED    17   3
  MAP3K5 WILD-TYPE 237  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED     17    3
  MAP3K5 WILD-TYPE  237   32
     clus
vv    MAP3K5 MUTATED MAP3K5 WILD-TYPE
  NO              17              237
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K5 MUTATED       0                         0    20
  MAP3K5 WILD-TYPE     5                         1   264
D110V13, multiclass
                           clus
vv                          MAP3K5 MUTATED MAP3K5 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 20              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"
D110V14, binary
                  cls
clus                 0   1
  MAP3K5 MUTATED     0  20
  MAP3K5 WILD-TYPE   3 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K5 MUTATED      0   20
  MAP3K5 WILD-TYPE    3  263
                        clus
vv                       MAP3K5 MUTATED MAP3K5 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             20              263
[1] 2 2
[1] FALSE

Clustering(111) Variable = NTN4 MUTATION ANALYSIS
D111V1, survival
                sevent
clus2             0  1
  NTN4 MUTATED    8  4
  NTN4 WILD-TYPE 89 99
  NTN4 MUTATED NTN4 WILD-TYPE 
            12            188 
  NTN4 MUTATED NTN4 WILD-TYPE 
             4             99 
$`NTN4 MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-EE-A181 TCGA-EE-A183 
      134.40        36.85        31.89        49.35        20.38        26.24 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2MT TCGA-EE-A3AA TCGA-FS-A1ZZ TCGA-GN-A4U8 
        0.26        47.74        23.51       124.31         3.06        46.92 

$`NTN4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       52.90        27.35        19.04         8.42        15.72       110.93 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        19.04        76.41        62.60        25.64        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH 
       62.86        15.75       168.00        86.30       107.61        36.30 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB 
      171.58        64.83        66.08        43.53        58.06       140.98 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       40.01        59.70        24.53         9.34        90.21        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       42.05        45.70       177.86        15.02        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        0.00        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       68.65        10.62        32.48        18.35        93.63         0.76 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.20        71.31        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       23.77       209.79        94.19       171.85        63.25        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
      104.78       145.45       227.01       143.93        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      184.60       150.12        99.06        59.84        42.51       120.76 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.71        47.18       146.63        73.05        22.36         4.70 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.87        10.19        28.67       173.29        68.52        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05        74.47         4.50       174.21       171.78        49.74 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
      195.98         8.35        27.62       312.07        32.78        43.92 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.82        36.33        78.61       130.95       136.27        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-OD-A75X TCGA-QB-A6FS 
       42.48         7.59       120.53        34.49       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  NTN4 MUTATED NTN4 WILD-TYPE 
          0.26           0.00 
  NTN4 MUTATED NTN4 WILD-TYPE 
        134.40         346.49 
  NTN4 MUTATED NTN4 WILD-TYPE 
        34.370         49.725 
[1] "0.3 - 134.4 (34.4)" "0.0 - 346.5 (49.7)"
[1] "hr=" "1"  
D111V2, survival
                sevent
clus2              0   1
  NTN4 MUTATED     8   6
  NTN4 WILD-TYPE 116 154
  NTN4 MUTATED NTN4 WILD-TYPE 
            14            270 
  NTN4 MUTATED NTN4 WILD-TYPE 
             6            154 
$`NTN4 MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-EE-A181 TCGA-EE-A183 
      134.40        36.95       112.04        71.80        33.73        26.89 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A2MT TCGA-EE-A3AA TCGA-FS-A1ZZ 
       63.78        56.84        39.29        71.21       124.31        27.02 
TCGA-GN-A266 TCGA-GN-A4U8 
       10.13        48.89 

$`NTN4 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       126.81        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       31.40        50.76        15.45        16.57        16.67       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        66.48 
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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       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 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 
       36.46        29.82        27.22         8.65        14.70         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       78.97        13.97        72.07        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82       115.96        59.64        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48       102.12        13.91        42.77        81.21 
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       180.39       216.66       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      248.65        43.23       162.48        53.26       122.73        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       28.77        54.51        13.81        41.59       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-A199 
       51.35       134.33       152.81        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 
      302.07       152.35         6.44       131.51        61.05        44.09 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        26.56        49.48        27.09        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        34.03        26.73        54.41        80.68 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       17.46        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        2.04        15.78       139.89       117.93        96.92        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       62.79        32.48        48.00       121.91        39.35        10.42 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
       22.13       297.90         7.23         0.20         0.33         0.69 

  NTN4 MUTATED NTN4 WILD-TYPE 
         10.13           0.20 
  NTN4 MUTATED NTN4 WILD-TYPE 
        134.40         369.93 
  NTN4 MUTATED NTN4 WILD-TYPE 
        52.865         53.970 
[1] "10.1 - 134.4 (52.9)" "0.2 - 369.9 (54.0)" 
[1] "hr=" "1.1"
D111V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  NTN4 MUTATED          0       2       1        0        3        1         0
  NTN4 WILD-TYPE       10       4      24       10       22       17        10
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NTN4 MUTATED           1         0         3          0          1          1
  NTN4 WILD-TYPE        13        10        33         14         25         42
                vv
clus             STAGE IV
  NTN4 MUTATED          0
  NTN4 WILD-TYPE       16
D111V4, multiclass
            clus
vv           NTN4 MUTATED NTN4 WILD-TYPE
  I/II NOS              0             10
  STAGE 0               2              4
  STAGE I               1             24
  STAGE IA              0             10
  STAGE IB              3             22
  STAGE II              1             17
  STAGE IIA             0             10
  STAGE IIB             1             13
  STAGE IIC             0             10
  STAGE III             3             33
  STAGE IIIA            0             14
  STAGE IIIB            1             25
  STAGE IIIC            1             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
  NTN4 MUTATED       1  5  3  1
  NTN4 WILD-TYPE    52 57 57 54
D111V5, multiclass
       clus
vv      NTN4 MUTATED NTN4 WILD-TYPE
  T0+T1            1             52
  T2               5             57
  T3               3             57
  T4               1             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NTN4 MUTATED     8   3   2   0
  NTN4 WILD-TYPE 135  50  32  35
D111V6, multiclass
    clus
vv   NTN4 MUTATED NTN4 WILD-TYPE
  N0            8            135
  N1            3             50
  N2            2             32
  N3            0             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"
D111V7, binary
                cls
clus               0   1
  NTN4 MUTATED    13   0
  NTN4 WILD-TYPE 243  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED     13    0
  NTN4 WILD-TYPE  243   17
   clus
vv  NTN4 MUTATED NTN4 WILD-TYPE
  0           13            243
  1            0             17
[1] 2 2
[1] FALSE
D111V8, binary
                cls
clus               0   1
  NTN4 MUTATED     5   2
  NTN4 WILD-TYPE 102  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      5    2
  NTN4 WILD-TYPE  102   71
     clus
vv    NTN4 MUTATED NTN4 WILD-TYPE
  NO             5            102
  YES            2             71
[1] 2 2
[1] FALSE
D111V9, binary
                cls
clus               0   1
  NTN4 MUTATED     2  13
  NTN4 WILD-TYPE  35 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      2   13
  NTN4 WILD-TYPE   35  240
     clus
vv    NTN4 MUTATED NTN4 WILD-TYPE
  NO             2             35
  YES           13            240
[1] 2 2
[1] FALSE
D111V10, continuous
D111V11, binary
                cls
clus               0   1
  NTN4 MUTATED     4  11
  NTN4 WILD-TYPE 105 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      4   11
  NTN4 WILD-TYPE  105  170
        clus
vv       NTN4 MUTATED NTN4 WILD-TYPE
  FEMALE            4            105
  MALE             11            170
[1] 2 2
[1] FALSE
D111V12, binary
                cls
clus               0   1
  NTN4 MUTATED    10   5
  NTN4 WILD-TYPE 244  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED     10    5
  NTN4 WILD-TYPE  244   30
     clus
vv    NTN4 MUTATED NTN4 WILD-TYPE
  NO            10            244
  YES            5             30
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NTN4 MUTATED       0                         0    15
  NTN4 WILD-TYPE     5                         1   269
D111V13, multiclass
                           clus
vv                          NTN4 MUTATED NTN4 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                               15            269
[1] 3 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
  NTN4 MUTATED     1  14
  NTN4 WILD-TYPE   2 269
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      1   14
  NTN4 WILD-TYPE    2  269
                        clus
vv                       NTN4 MUTATED NTN4 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           14            269
[1] 2 2
[1] FALSE

Clustering(112) Variable = BCMO1 MUTATION ANALYSIS
D112V1, survival
                 sevent
clus2              0  1
  BCMO1 MUTATED    8  5
  BCMO1 WILD-TYPE 89 98
  BCMO1 MUTATED BCMO1 WILD-TYPE 
             13             187 
  BCMO1 MUTATED BCMO1 WILD-TYPE 
              5              98 
$`BCMO1 MUTATED`
TCGA-EE-A2GO TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-EE-A20F TCGA-EE-A2MT 
       52.90        36.85        62.86        76.34        79.20        23.51 
TCGA-ER-A19G TCGA-ER-A19N TCGA-FS-A1ZC TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-GN-A267 
      184.60        42.51       312.07       136.27         3.06        17.06 
TCGA-GN-A4U3 
      120.53 

$`BCMO1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
      134.40        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       25.64        45.99        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       23.67       173.85        30.67       144.46        31.76        62.70 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.34        42.05        45.70       177.86        15.02        22.29 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       69.21        22.85       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       60.10        64.83        58.85        30.44       225.11        42.64 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.91        16.41        52.41        18.21        13.15        24.89 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C 
       20.38         0.00        26.24        75.55        75.22        76.14 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       12.99         0.26        44.28        47.41        47.74        27.16 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       61.12       346.49       185.19       115.43        30.02        77.98 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       26.14        12.95       201.60        68.65        10.62        32.48 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       18.35        93.63         0.76         0.20        71.31        81.99 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG 
      103.13        15.25         5.75        23.77       209.79        94.19 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      171.85        63.25        89.26       104.78       145.45       227.01 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      143.93        53.26       124.31       122.73        64.04         4.41 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       54.51         6.28        67.89       111.85        45.90         3.35 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      168.85        19.86       135.98        34.45        10.49         7.82 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19L 
        4.54        53.29        39.81        11.47       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       59.84       120.76        49.71        47.18       146.63        73.05 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       22.36         4.70        16.87        10.19        28.67       173.29 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       68.52        15.48        32.05        74.47         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZD 
      171.78        49.74       195.98         8.35        27.62        32.78 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       43.92         7.82        36.33        78.61       130.95        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
        4.47        23.21         5.29        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       18.25         1.91        53.29       117.93        96.92        42.48 
TCGA-GN-A26A TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
        7.59        34.49        46.92       297.01         7.23         0.20 
TCGA-RP-A693 
        0.33 

  BCMO1 MUTATED BCMO1 WILD-TYPE 
           3.06            0.00 
  BCMO1 MUTATED BCMO1 WILD-TYPE 
         312.07          346.49 
  BCMO1 MUTATED BCMO1 WILD-TYPE 
          62.86           46.92 
[1] "3.1 - 312.1 (62.9)" "0.0 - 346.5 (46.9)"
[1] "hr=" "2"  
D112V2, survival
                 sevent
clus2               0   1
  BCMO1 MUTATED     8   9
  BCMO1 WILD-TYPE 116 151
  BCMO1 MUTATED BCMO1 WILD-TYPE 
             17             267 
  BCMO1 MUTATED BCMO1 WILD-TYPE 
              9             151 
$`BCMO1 MUTATED`
TCGA-EE-A2GO TCGA-FW-A3R5 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-EE-A20F TCGA-EE-A2MT 
      126.81        36.95        65.49        76.57        91.56        71.21 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19N TCGA-FS-A1ZC 
       36.95        53.19        26.37       302.07        44.09       357.37 
TCGA-FS-A1ZK TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-GN-A267 TCGA-GN-A4U3 
       23.93       148.80        27.02        64.44       121.91 

$`BCMO1 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2MR TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       134.40        27.35 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74        43.43       103.10        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       77.56        22.95        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       133.81       151.27        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        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        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
       59.64        39.29        86.14        59.28        67.43       173.79 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      220.24        48.72       107.38        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      102.12        13.91        42.77        81.21        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 
      180.39       216.66       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        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       138.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        51.35       134.33       152.81 
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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59        13.02       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        49.48         8.88       148.18       105.07 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        28.83        48.99        41.56 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L 
      247.04        93.01        46.98        33.21        12.95       149.03 
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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        46.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73       133.55        11.41        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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        10.13        62.79        32.48        48.00 
TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.35        10.42        48.89        22.13       297.90         7.23 
TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        0.20         0.33         0.69 

  BCMO1 MUTATED BCMO1 WILD-TYPE 
          23.93            0.20 
  BCMO1 MUTATED BCMO1 WILD-TYPE 
         357.37          369.93 
  BCMO1 MUTATED BCMO1 WILD-TYPE 
          65.49           53.52 
[1] "23.9 - 357.4 (65.5)" "0.2 - 369.9 (53.5)" 
[1] "hr=" "1.5"
D112V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  BCMO1 MUTATED          1       0       2        0        3        2         0
  BCMO1 WILD-TYPE        9       6      23       10       22       16        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BCMO1 MUTATED           1         0         3          1          1
  BCMO1 WILD-TYPE        13        10        33         13         25
                 vv
clus              STAGE IIIC STAGE IV
  BCMO1 MUTATED            0        0
  BCMO1 WILD-TYPE         43       16
D112V4, multiclass
            clus
vv           BCMO1 MUTATED BCMO1 WILD-TYPE
  I/II NOS               1               9
  STAGE 0                0               6
  STAGE I                2              23
  STAGE IA               0              10
  STAGE IB               3              22
  STAGE II               2              16
  STAGE IIA              0              10
  STAGE IIB              1              13
  STAGE IIC              0              10
  STAGE III              3              33
  STAGE IIIA             1              13
  STAGE IIIB             1              25
  STAGE IIIC             0              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
  BCMO1 MUTATED       2  4  3  3
  BCMO1 WILD-TYPE    51 58 57 52
D112V5, multiclass
       clus
vv      BCMO1 MUTATED BCMO1 WILD-TYPE
  T0+T1             2              51
  T2                4              58
  T3                3              57
  T4                3              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BCMO1 MUTATED    11   3   2   0
  BCMO1 WILD-TYPE 132  50  32  35
D112V6, multiclass
    clus
vv   BCMO1 MUTATED BCMO1 WILD-TYPE
  N0            11             132
  N1             3              50
  N2             2              32
  N3             0              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"
D112V7, binary
                 cls
clus                0   1
  BCMO1 MUTATED    16   0
  BCMO1 WILD-TYPE 240  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCMO1 MUTATED     16    0
  BCMO1 WILD-TYPE  240   17
   clus
vv  BCMO1 MUTATED BCMO1 WILD-TYPE
  0            16             240
  1             0              17
[1] 2 2
[1] FALSE
D112V8, binary
                 cls
clus               0  1
  BCMO1 MUTATED    8  1
  BCMO1 WILD-TYPE 99 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCMO1 MUTATED      8    1
  BCMO1 WILD-TYPE   99   72
     clus
vv    BCMO1 MUTATED BCMO1 WILD-TYPE
  NO              8              99
  YES             1              72
[1] 2 2
[1] FALSE
D112V9, binary
                 cls
clus                0   1
  BCMO1 MUTATED     2  15
  BCMO1 WILD-TYPE  35 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCMO1 MUTATED      2   15
  BCMO1 WILD-TYPE   35  238
     clus
vv    BCMO1 MUTATED BCMO1 WILD-TYPE
  NO              2              35
  YES            15             238
[1] 2 2
[1] FALSE
D112V10, continuous
D112V11, binary
                 cls
clus                0   1
  BCMO1 MUTATED     4  13
  BCMO1 WILD-TYPE 105 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCMO1 MUTATED      4   13
  BCMO1 WILD-TYPE  105  168
        clus
vv       BCMO1 MUTATED BCMO1 WILD-TYPE
  FEMALE             4             105
  MALE              13             168
[1] 2 2
[1] FALSE
D112V12, binary
                 cls
clus                0   1
  BCMO1 MUTATED    12   5
  BCMO1 WILD-TYPE 242  30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCMO1 MUTATED     12    5
  BCMO1 WILD-TYPE  242   30
     clus
vv    BCMO1 MUTATED BCMO1 WILD-TYPE
  NO             12             242
  YES             5              30
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCMO1 MUTATED       0                         0    17
  BCMO1 WILD-TYPE     5                         1   267
D112V13, multiclass
                           clus
vv                          BCMO1 MUTATED BCMO1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                17             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"
D112V14, binary
                 cls
clus                0   1
  BCMO1 MUTATED     1  16
  BCMO1 WILD-TYPE   2 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCMO1 MUTATED      1   16
  BCMO1 WILD-TYPE    2  267
                        clus
vv                       BCMO1 MUTATED BCMO1 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO            16             267
[1] 2 2
[1] FALSE

Clustering(113) Variable = OR11H12 MUTATION ANALYSIS
D113V1, survival
                   sevent
clus2                0  1
  OR11H12 MUTATED    6  6
  OR11H12 WILD-TYPE 91 97
  OR11H12 MUTATED OR11H12 WILD-TYPE 
               12               188 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                6                97 
$`OR11H12 MUTATED`
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A3MU TCGA-D9-A3Z1 TCGA-EE-A29D 
      134.40        19.04        36.85        23.67        15.02        12.99 
TCGA-EE-A29P TCGA-EE-A2GS TCGA-EE-A2MI TCGA-EE-A2MS TCGA-ER-A19D TCGA-ER-A19S 
       27.16        71.31       171.85       143.93        11.47        47.18 

$`OR11H12 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       52.90        27.35         8.42        15.72        31.89       110.93 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       49.35       133.25        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      140.98        40.01        59.70        24.53         9.34        90.21 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       42.05        45.70       177.86        22.29        69.21        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       76.34       138.67        68.68       150.61       110.53        60.10 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       64.83        58.85        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 
       16.41        52.41        18.21        13.15        24.89        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
        0.00        26.24        75.55        79.20        75.22        76.14 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        44.28        47.41        47.74        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        0.76         0.20        81.99       103.13        15.25         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79        94.19        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      145.45       227.01        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
       10.49         7.82         4.54        53.29        39.81       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      146.63        73.05        22.36         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L 
       28.67       173.29        68.52        15.48        32.05        74.47 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.50       174.21       171.78        49.74       195.98         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  OR11H12 MUTATED OR11H12 WILD-TYPE 
            11.47              0.00 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
           171.85            346.49 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
           32.005            48.545 
[1] "11.5 - 171.8 (32.0)" "0.0 - 346.5 (48.5)" 
[1] "hr=" "1.1"
D113V2, survival
                   sevent
clus2                 0   1
  OR11H12 MUTATED     8   7
  OR11H12 WILD-TYPE 116 153
  OR11H12 MUTATED OR11H12 WILD-TYPE 
               15               269 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                7               153 
$`OR11H12 MUTATED`
TCGA-EE-A2MR TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D9-A3Z1 
      134.40        31.40        36.95        39.75        45.30        15.39 
TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2GS TCGA-EE-A2MI TCGA-EE-A2MS 
       13.97        56.42        25.87        81.21       204.66       162.48 
TCGA-ER-A19D TCGA-ER-A19S TCGA-GF-A6C9 
       12.59        49.48        15.78 

$`OR11H12 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD 
       68.15       168.26         2.60       340.14       126.81        27.35 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       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         7.10 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       78.97        63.78        72.07        64.64        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       66.74        14.47        61.28       369.93       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       115.96        59.64        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       173.79       220.24        48.72       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       79.66        75.48       102.12        13.91        42.77        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-A2MJ 
       47.28       103.27       268.73       103.20        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      180.39       216.66       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        64.04        28.77 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        41.59       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-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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        46.45 
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 
       34.03        26.73        54.41        80.68        17.46        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       13.51        19.30         9.90        19.43         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        96.92        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  OR11H12 MUTATED OR11H12 WILD-TYPE 
            12.59              0.20 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
           204.66            369.93 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
            39.75             54.51 
[1] "12.6 - 204.7 (39.8)" "0.2 - 369.9 (54.5)" 
[1] "hr=" "1"  
D113V3, continuous
                   vv
clus                I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  OR11H12 MUTATED          0       0       1        0        2        1
  OR11H12 WILD-TYPE       10       6      24       10       23       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  OR11H12 MUTATED           0         2         1         1          1
  OR11H12 WILD-TYPE        10        12         9        35         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  OR11H12 MUTATED            2          3        0
  OR11H12 WILD-TYPE         24         40       16
D113V4, multiclass
            clus
vv           OR11H12 MUTATED OR11H12 WILD-TYPE
  I/II NOS                 0                10
  STAGE 0                  0                 6
  STAGE I                  1                24
  STAGE IA                 0                10
  STAGE IB                 2                23
  STAGE II                 1                17
  STAGE IIA                0                10
  STAGE IIB                2                12
  STAGE IIC                1                 9
  STAGE III                1                35
  STAGE IIIA               1                13
  STAGE IIIB               2                24
  STAGE IIIC               3                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
  OR11H12 MUTATED       0  5  5  2
  OR11H12 WILD-TYPE    53 57 55 53
D113V5, multiclass
       clus
vv      OR11H12 MUTATED OR11H12 WILD-TYPE
  T0+T1               0                53
  T2                  5                57
  T3                  5                55
  T4                  2                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  OR11H12 MUTATED     7   2   3   1
  OR11H12 WILD-TYPE 136  51  31  34
D113V6, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  N0               7               136
  N1               2                51
  N2               3                31
  N3               1                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"
D113V7, binary
                   cls
clus                  0   1
  OR11H12 MUTATED    13   0
  OR11H12 WILD-TYPE 243  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED     13    0
  OR11H12 WILD-TYPE  243   17
   clus
vv  OR11H12 MUTATED OR11H12 WILD-TYPE
  0              13               243
  1               0                17
[1] 2 2
[1] FALSE
D113V8, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     6   4
  OR11H12 WILD-TYPE 101  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      6    4
  OR11H12 WILD-TYPE  101   69
     clus
vv    OR11H12 MUTATED OR11H12 WILD-TYPE
  NO                6               101
  YES               4                69
[1] 2 2
[1] FALSE
D113V9, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     2  13
  OR11H12 WILD-TYPE  35 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      2   13
  OR11H12 WILD-TYPE   35  240
     clus
vv    OR11H12 MUTATED OR11H12 WILD-TYPE
  NO                2                35
  YES              13               240
[1] 2 2
[1] FALSE
D113V10, continuous
D113V11, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     5  10
  OR11H12 WILD-TYPE 104 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      5   10
  OR11H12 WILD-TYPE  104  171
        clus
vv       OR11H12 MUTATED OR11H12 WILD-TYPE
  FEMALE               5               104
  MALE                10               171
[1] 2 2
[1] FALSE
D113V12, binary
                   cls
clus                  0   1
  OR11H12 MUTATED    13   2
  OR11H12 WILD-TYPE 241  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED     13    2
  OR11H12 WILD-TYPE  241   33
     clus
vv    OR11H12 MUTATED OR11H12 WILD-TYPE
  NO               13               241
  YES               2                33
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR11H12 MUTATED       0                         0    15
  OR11H12 WILD-TYPE     5                         1   269
D113V13, multiclass
                           clus
vv                          OR11H12 MUTATED OR11H12 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  15               269
[1] 3 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
  OR11H12 MUTATED     0  15
  OR11H12 WILD-TYPE   3 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      0   15
  OR11H12 WILD-TYPE    3  268
                        clus
vv                       OR11H12 MUTATED OR11H12 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               268
[1] 2 2
[1] FALSE

Clustering(114) Variable = SI MUTATION ANALYSIS
D114V1, survival
              sevent
clus2           0  1
  SI MUTATED   27 19
  SI WILD-TYPE 70 84
  SI MUTATED SI WILD-TYPE 
          46          154 
  SI MUTATED SI WILD-TYPE 
          19           84 
$`SI MUTATED`
TCGA-D3-A3C8 TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QA 
       38.76        27.35        36.85       110.93        49.35        76.41 
TCGA-D3-A3MR TCGA-D3-A51T TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1I7 
       90.21        11.34       177.86        15.02        69.21        60.10 
TCGA-DA-A3F8 TCGA-EB-A5UN TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B 
       42.64        52.41         0.00        26.24        79.20        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2GE TCGA-EE-A2GM 
       76.14        12.99         0.26        47.74        12.95        18.35 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AA 
        0.76         0.20       103.13        63.25       143.93       124.31 
TCGA-EE-A3AE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19P TCGA-ER-A2NC 
       54.51       135.98        34.45         7.82       120.76        22.36 
TCGA-ER-A3ET TCGA-ER-A42L TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 
       68.52        74.47        23.21         3.06        18.51        13.28 
TCGA-GF-A6C8 TCGA-GN-A4U3 TCGA-QB-A6FS TCGA-RP-A693 
        1.91       120.53         7.23         0.33 

$`SI WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        33.24        31.96       166.75       269.03        52.90 
TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
      134.40        19.04         8.42        15.72        31.89       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       19.04        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J 
       24.53         9.34        23.67       173.85        30.67       144.46 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A3Z3 TCGA-D9-A6EG 
       31.76        62.70        42.05        45.70        22.29        22.85 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IA 
       76.34       138.67        68.68       150.61       110.53        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 
       58.85        30.44       225.11         3.91        16.41        18.21 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H 
       13.15        24.89        20.38        75.55        44.28        47.41 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       77.98        26.14       201.60        68.65        10.62        32.48 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       93.63        71.31        81.99        15.25         5.75        23.77 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      209.79        94.19       171.85        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      227.01        23.51        53.26       122.73        64.04         4.41 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       19.86        10.49         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84        42.51        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       47.18       146.63        73.05         4.70        16.87        10.19 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       28.67       173.29        15.48        32.05         4.50       174.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC 
      171.78        49.74       195.98         8.35        27.62       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       32.78        43.92         7.82        36.33        78.61       130.95 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F8 
      136.27        35.28         4.47         5.29        66.67       173.19 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       53.29       117.93        96.92        17.06        42.48         7.59 
TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A690 
       34.49        46.92       297.01         0.20 

  SI MUTATED SI WILD-TYPE 
         0.0          0.2 
  SI MUTATED SI WILD-TYPE 
      177.86       346.49 
  SI MUTATED SI WILD-TYPE 
       40.70        48.56 
[1] "0.0 - 177.9 (40.7)" "0.2 - 346.5 (48.6)"
[1] "hr=" "1.1"
D114V2, survival
              sevent
clus2            0   1
  SI MUTATED    33  32
  SI WILD-TYPE  91 128
  SI MUTATED SI WILD-TYPE 
          65          219 
  SI MUTATED SI WILD-TYPE 
          32          128 
$`SI MUTATED`
TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A184 TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q5 
       46.32        13.87        68.15        27.35        36.95       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A3MR TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR 
       71.80        90.90       103.59        26.89       137.92       178.32 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EB-A5UN 
      125.19        15.39        77.56        88.87        43.36        58.92 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C 
       14.70        26.89         4.96        91.56        85.08        78.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       13.97        63.78        56.84        14.47        61.28        25.87 
TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GP 
       46.82        67.43       173.79        48.72        75.48        13.91 
TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AA 
       42.77       129.27        47.28        96.23       162.48       124.31 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19F 
       54.51        36.95       152.81        35.44         9.17        26.37 
TCGA-ER-A19P TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A42L TCGA-FS-A1ZA TCGA-FS-A1ZK 
      162.08        43.82        93.01       149.03        27.72        23.93 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       49.48        27.02        77.82        34.03        54.41        17.46 
TCGA-GF-A6C8 TCGA-GN-A266 TCGA-GN-A4U3 TCGA-QB-A6FS TCGA-RP-A693 
        2.04        10.13       121.91         7.23         0.33 

$`SI WILD-TYPE`
TCGA-D3-A2JF TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L 
       62.07        68.25        54.02        94.98       168.26         2.60 
TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF 
      340.14       126.81       134.40        31.40        50.76        15.45 
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.04       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-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-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        66.48        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.98       166.52        86.93        60.23        24.53         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-A5GL TCGA-D3-A5GN TCGA-D3-A5GS 
       32.94        22.62        63.81       125.79       135.75        18.18 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53        54.67         3.65         7.10        22.29         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        22.95        76.57        36.03       144.89        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      222.51       176.55        35.93       135.02        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       40.60        68.09        33.93        10.49       225.96        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       10.36        20.35        29.29         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I 
       27.22         8.65        33.73       133.81       151.27        13.55 
TCGA-EE-A29A TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.35        72.07        64.64        18.61        56.42        66.74 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      369.93       195.02        17.92       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       86.14        59.28       220.24       107.38        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
      102.12        81.21        44.88        94.82        21.67        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       180.39       216.66       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       43.23        71.21        53.26       122.73        64.04        28.77 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        41.59       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A197 
       34.32        53.19       201.80        51.35       134.33        13.94 
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       302.07 
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        44.09        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       49.48         8.88       148.18       105.07        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       28.83        48.99        41.56       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX 
       12.95        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        46.45         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-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       26.56        27.09        66.67        28.73       174.84        26.73 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        13.51        19.30         9.90        19.43 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.78       139.89       117.93        96.92        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       32.48        48.00        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-RP-A690 TCGA-RP-A694 
      297.90         0.20         0.69 

  SI MUTATED SI WILD-TYPE 
        0.33         0.20 
  SI MUTATED SI WILD-TYPE 
      178.32       369.93 
  SI MUTATED SI WILD-TYPE 
       49.48        54.02 
[1] "0.3 - 178.3 (49.5)" "0.2 - 369.9 (54.0)"
[1] "hr=" "1"  
D114V3, continuous
              vv
clus           I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SI MUTATED          1       2       4        2        6        6         3
  SI WILD-TYPE        9       4      21        8       19       12         7
              vv
clus           STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SI MUTATED           5         2         9          3          6         11
  SI WILD-TYPE         9         8        27         11         20         32
              vv
clus           STAGE IV
  SI MUTATED          3
  SI WILD-TYPE       13
D114V4, multiclass
            clus
vv           SI MUTATED SI WILD-TYPE
  I/II NOS            1            9
  STAGE 0             2            4
  STAGE I             4           21
  STAGE IA            2            8
  STAGE IB            6           19
  STAGE II            6           12
  STAGE IIA           3            7
  STAGE IIB           5            9
  STAGE IIC           2            8
  STAGE III           9           27
  STAGE IIIA          3           11
  STAGE IIIB          6           20
  STAGE IIIC         11           32
  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
  SI MUTATED      10 10 18 16
  SI WILD-TYPE    43 52 42 39
D114V5, multiclass
       clus
vv      SI MUTATED SI WILD-TYPE
  T0+T1         10           43
  T2            10           52
  T3            18           42
  T4            16           39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2  N3
  SI MUTATED    34  15   7   6
  SI WILD-TYPE 109  38  27  29
D114V6, multiclass
    clus
vv   SI MUTATED SI WILD-TYPE
  N0         34          109
  N1         15           38
  N2          7           27
  N3          6           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"
D114V7, binary
              cls
clus             0   1
  SI MUTATED    63   3
  SI WILD-TYPE 193  14
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED     63    3
  SI WILD-TYPE  193   14
   clus
vv  SI MUTATED SI WILD-TYPE
  0         63          193
  1          3           14
[1] 2 2
[1] FALSE
D114V8, binary
              cls
clus            0  1
  SI MUTATED   24 18
  SI WILD-TYPE 83 55
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED     24   18
  SI WILD-TYPE   83   55
     clus
vv    SI MUTATED SI WILD-TYPE
  NO          24           83
  YES         18           55
[1] 2 2
[1] FALSE
D114V9, binary
              cls
clus             0   1
  SI MUTATED     8  59
  SI WILD-TYPE  29 194
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED      8   59
  SI WILD-TYPE   29  194
     clus
vv    SI MUTATED SI WILD-TYPE
  NO           8           29
  YES         59          194
[1] 2 2
[1] FALSE
D114V10, continuous
D114V11, binary
              cls
clus             0   1
  SI MUTATED    19  48
  SI WILD-TYPE  90 133
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED     19   48
  SI WILD-TYPE   90  133
        clus
vv       SI MUTATED SI WILD-TYPE
  FEMALE         19           90
  MALE           48          133
[1] 2 2
[1] FALSE
D114V12, binary
              cls
clus             0   1
  SI MUTATED    58   9
  SI WILD-TYPE 196  26
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED     58    9
  SI WILD-TYPE  196   26
     clus
vv    SI MUTATED SI WILD-TYPE
  NO          58          196
  YES          9           26
[1] 2 2
[1] FALSE
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SI MUTATED       0                         0    67
  SI WILD-TYPE     5                         1   217
D114V13, multiclass
                           clus
vv                          SI MUTATED SI WILD-TYPE
  ASIAN                              0            5
  BLACK OR AFRICAN AMERICAN          0            1
  WHITE                             67          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"
D114V14, binary
              cls
clus             0   1
  SI MUTATED     1  66
  SI WILD-TYPE   2 217
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED      1   66
  SI WILD-TYPE    2  217
                        clus
vv                       SI MUTATED SI WILD-TYPE
  HISPANIC OR LATINO              1            2
  NOT HISPANIC OR LATINO         66          217
[1] 2 2
[1] FALSE

Clustering(115) Variable = ADAM33 MUTATION ANALYSIS
D115V1, survival
                  sevent
clus2               0  1
  ADAM33 MUTATED    5  7
  ADAM33 WILD-TYPE 92 96
  ADAM33 MUTATED ADAM33 WILD-TYPE 
              12              188 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
               7               96 
$`ADAM33 MUTATED`
TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q7 TCGA-D3-A3MR TCGA-DA-A1IC TCGA-EE-A181 
       27.35        36.85       133.25        90.21        58.85        20.38 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2GP TCGA-EE-A2GR TCGA-ER-A19P TCGA-GN-A26A 
        0.26        47.74         0.76         0.20       120.76         7.59 

$`ADAM33 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90       134.40        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.93        49.35        19.04        76.41        62.60        25.64 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       45.99        62.86        15.75       168.00        86.30       107.61 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       36.30       171.58        64.83        66.08        43.53        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU 
      140.98        40.01        59.70        24.53         9.34        23.67 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      173.85        30.67       144.46        31.76        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       42.05        45.70       177.86        15.02        22.29        69.21 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       22.85        76.34       138.67        68.68       150.61       110.53 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       60.10        64.83        30.44       225.11        42.64         3.91 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 
       16.41        52.41        18.21        13.15        24.89         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       44.28        47.41        27.16        61.12       346.49       185.19 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS 
       68.65        10.62        32.48        18.35        93.63        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       45.90         3.35       168.85        19.86       135.98        34.45 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       10.49         7.82         4.54        53.29        39.81        11.47 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      184.60       150.12        99.06        59.84        42.51        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       74.47         4.50       174.21       171.78        49.74       195.98 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        8.35        27.62       312.07        32.78        43.92         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       36.33        78.61       130.95       136.27        35.28         4.47 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.21         5.29         3.06        18.51        66.67       173.19 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       13.28        80.68        55.59        11.54        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       18.25         1.91        53.29       117.93        96.92        17.06 
TCGA-GN-A268 TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       42.48       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  ADAM33 MUTATED ADAM33 WILD-TYPE 
             0.2              0.0 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
          133.25           346.49 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
           32.10            48.38 
[1] "0.2 - 133.2 (32.1)" "0.0 - 346.5 (48.4)"
[1] "hr=" "1.8"
D115V2, survival
                  sevent
clus2                0   1
  ADAM33 MUTATED     6   9
  ADAM33 WILD-TYPE 118 151
  ADAM33 MUTATED ADAM33 WILD-TYPE 
              15              269 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
               9              151 
$`ADAM33 MUTATED`
TCGA-EE-A3JD TCGA-FW-A3R5 TCGA-D3-A1Q7 TCGA-D3-A3MR TCGA-DA-A1IC TCGA-EE-A181 
       27.35        36.95       133.25       103.59        68.09        33.73 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A3AG 
       63.78        56.84        48.72        13.91        42.77        41.59 
TCGA-ER-A19P TCGA-GN-A266 TCGA-GN-A26A 
      162.08        10.13        32.48 

$`ADAM33 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       31.40        50.76        15.45        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       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 
        7.10        15.39        22.29         9.90        25.18        77.56 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        76.57        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       40.60        33.93        10.49       225.96        43.36        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       10.36        20.35        29.29        58.92         7.04        36.46 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       29.82        27.22         8.65        14.70        26.89         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        85.08 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       78.97        13.97        72.07        64.64        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       66.74        14.47        61.28       369.93        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       115.96        59.64        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       173.79       220.24       107.38        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       79.66        75.48       102.12        81.21        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 
      180.39       216.66       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        64.04 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       28.77        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-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
      134.33       152.81        35.44        13.94         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       302.07 
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        44.09        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       46.45         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        34.03        26.73        54.41        80.68        17.46 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       55.59        13.51        19.30         9.90        19.43         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.78       139.89       117.93        96.92        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 
       48.00       121.91        39.35        10.42        48.89        22.13 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
      297.90         7.23         0.20         0.33         0.69 

  ADAM33 MUTATED ADAM33 WILD-TYPE 
           10.13             0.20 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
          162.08           369.93 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
           42.77            54.41 
[1] "10.1 - 162.1 (42.8)" "0.2 - 369.9 (54.4)" 
[1] "hr=" "1.4"
D115V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  ADAM33 MUTATED          0       1       0        1        2        2
  ADAM33 WILD-TYPE       10       5      25        9       23       16
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  ADAM33 MUTATED           0         0         0         4          1
  ADAM33 WILD-TYPE        10        14        10        32         13
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  ADAM33 MUTATED            3          0        0
  ADAM33 WILD-TYPE         23         43       16
D115V4, multiclass
            clus
vv           ADAM33 MUTATED ADAM33 WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 1                5
  STAGE I                 0               25
  STAGE IA                1                9
  STAGE IB                2               23
  STAGE II                2               16
  STAGE IIA               0               10
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               4               32
  STAGE IIIA              1               13
  STAGE IIIB              3               23
  STAGE IIIC              0               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
  ADAM33 MUTATED       4  1  4  2
  ADAM33 WILD-TYPE    49 61 56 53
D115V5, multiclass
       clus
vv      ADAM33 MUTATED ADAM33 WILD-TYPE
  T0+T1              4               49
  T2                 1               61
  T3                 4               56
  T4                 2               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ADAM33 MUTATED     7   4   4   0
  ADAM33 WILD-TYPE 136  49  30  35
D115V6, multiclass
    clus
vv   ADAM33 MUTATED ADAM33 WILD-TYPE
  N0              7              136
  N1              4               49
  N2              4               30
  N3              0               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"
D115V7, binary
                  cls
clus                 0   1
  ADAM33 MUTATED    15   0
  ADAM33 WILD-TYPE 241  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED     15    0
  ADAM33 WILD-TYPE  241   17
   clus
vv  ADAM33 MUTATED ADAM33 WILD-TYPE
  0             15              241
  1              0               17
[1] 2 2
[1] FALSE
D115V8, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     6   1
  ADAM33 WILD-TYPE 101  72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      6    1
  ADAM33 WILD-TYPE  101   72
     clus
vv    ADAM33 MUTATED ADAM33 WILD-TYPE
  NO               6              101
  YES              1               72
[1] 2 2
[1] FALSE
D115V9, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     4  12
  ADAM33 WILD-TYPE  33 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      4   12
  ADAM33 WILD-TYPE   33  241
     clus
vv    ADAM33 MUTATED ADAM33 WILD-TYPE
  NO               4               33
  YES             12              241
[1] 2 2
[1] FALSE
D115V10, continuous
D115V11, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     5  11
  ADAM33 WILD-TYPE 104 170
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      5   11
  ADAM33 WILD-TYPE  104  170
        clus
vv       ADAM33 MUTATED ADAM33 WILD-TYPE
  FEMALE              5              104
  MALE               11              170
[1] 2 2
[1] FALSE
D115V12, binary
                  cls
clus                 0   1
  ADAM33 MUTATED    14   2
  ADAM33 WILD-TYPE 240  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED     14    2
  ADAM33 WILD-TYPE  240   33
     clus
vv    ADAM33 MUTATED ADAM33 WILD-TYPE
  NO              14              240
  YES              2               33
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM33 MUTATED       0                         0    16
  ADAM33 WILD-TYPE     5                         1   268
D115V13, multiclass
                           clus
vv                          ADAM33 MUTATED ADAM33 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 16              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"
D115V14, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     0  16
  ADAM33 WILD-TYPE   3 267
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      0   16
  ADAM33 WILD-TYPE    3  267
                        clus
vv                       ADAM33 MUTATED ADAM33 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             16              267
[1] 2 2
[1] FALSE

Clustering(116) Variable = RICTOR MUTATION ANALYSIS
D116V1, survival
                  sevent
clus2                0   1
  RICTOR MUTATED     5   1
  RICTOR WILD-TYPE  92 102
  RICTOR MUTATED RICTOR WILD-TYPE 
               6              194 
  RICTOR MUTATED RICTOR WILD-TYPE 
               1              102 
$`RICTOR MUTATED`
TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-DA-A1HV TCGA-EE-A20F TCGA-EE-A3JB TCGA-FS-A1Z0 
      134.40        36.85        76.34        79.20       168.85       195.98 

$`RICTOR WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       52.90        27.35        19.04         8.42        15.72        31.89 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      110.93        49.35       133.25        19.04        76.41        62.60 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       25.64        45.99        62.86        15.75       168.00        86.30 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      107.61        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       58.06       140.98        40.01        59.70        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
       90.21        23.67       173.85        30.67       144.46        31.76 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 
       62.70        11.34        42.05        45.70       177.86        15.02 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.29        69.21        22.85       138.67        68.68       150.61 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
      110.53        60.10        64.83        58.85        30.44       225.11 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       42.64         3.91        16.41        52.41        18.21        13.15 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29B 
       24.89        20.38         0.00        26.24        75.55        75.22 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       76.14        12.99         0.26        44.28        47.41        47.74 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       27.16        61.12       346.49       185.19       115.43        30.02 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       77.98        26.14        12.95       201.60        68.65        10.62 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       32.48        18.35        93.63         0.76         0.20        71.31 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF 
       81.99       103.13        15.25         5.75        23.77       209.79 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       94.19       171.85        63.25        89.26       104.78       145.45 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      227.01       143.93        23.51        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 
       64.04         4.41        54.51         6.28        67.89       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       45.90         3.35        19.86       135.98        34.45        10.49 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G 
        7.82         4.54        53.29        39.81        11.47       184.60 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      150.12        99.06        59.84        42.51       120.76        49.71 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       47.18       146.63        73.05        22.36         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       10.19        28.67       173.29        68.52        15.48        32.05 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       74.47         4.50       174.21       171.78        49.74         8.35 
TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       27.62       312.07        32.78        43.92         7.82        36.33 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       78.61       130.95       136.27        35.28         4.47        23.21 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.29         3.06        18.51        66.67       173.19        13.28 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       80.68        55.59        11.54        19.30         9.90        18.25 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.91        53.29       117.93        96.92        17.06        42.48 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
        7.59       120.53        34.49        46.92       297.01         7.23 
TCGA-RP-A690 TCGA-RP-A693 
        0.20         0.33 

  RICTOR MUTATED RICTOR WILD-TYPE 
           36.85             0.00 
  RICTOR MUTATED RICTOR WILD-TYPE 
          195.98           346.49 
  RICTOR MUTATED RICTOR WILD-TYPE 
         106.800           46.455 
[1] "36.9 - 196.0 (106.8)" "0.0 - 346.5 (46.5)"  
[1] "hr=" "5.4"
D116V2, survival
                  sevent
clus2                0   1
  RICTOR MUTATED     6   6
  RICTOR WILD-TYPE 118 154
  RICTOR MUTATED RICTOR WILD-TYPE 
              12              272 
  RICTOR MUTATED RICTOR WILD-TYPE 
               6              154 
$`RICTOR MUTATED`
TCGA-EE-A184 TCGA-EE-A2MR TCGA-FW-A3R5 TCGA-DA-A1HV TCGA-EE-A20F TCGA-EE-A29S 
       68.15       134.40        36.95        76.57        91.56        61.28 
TCGA-EE-A29V TCGA-EE-A3JB TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-GF-A6C9 
       25.87       201.80       202.65        23.93        28.73        15.78 

$`RICTOR WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A3JD TCGA-ER-A193 
      168.26         2.60       340.14       126.81        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       50.76        15.45        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       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 
       66.48        66.08        59.57       130.72        58.06        46.98 
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-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-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       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         7.10        15.39        22.29         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       77.56        22.95        36.03       144.89        20.38       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       135.02        88.87        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       40.60        68.09        33.93        10.49       225.96        43.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.36        20.35        29.29        58.92         7.04 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       36.46        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A 
       26.89         4.96       133.81       151.27        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       85.08        78.97        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-A29T 
       56.84        18.61        56.42        66.74        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66 
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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32        53.19        51.35       134.33       152.81 
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       302.07       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        44.09       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18       105.07        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       28.83        48.99        41.56       247.04        93.01        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       33.21        12.95       149.03        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-A1ZG 
       27.72        48.85       357.37        53.52        46.45         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-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67       174.84        34.03        26.73        54.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       80.68        17.46        55.59        13.51        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       19.43         2.04       139.89       117.93        96.92        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U3 TCGA-GN-A4U4 
       64.44        62.79        32.48        48.00       121.91        39.35 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 
       10.42        48.89        22.13       297.90         7.23         0.20 
TCGA-RP-A693 TCGA-RP-A694 
        0.33         0.69 

  RICTOR MUTATED RICTOR WILD-TYPE 
           15.78             0.20 
  RICTOR MUTATED RICTOR WILD-TYPE 
          202.65           369.93 
  RICTOR MUTATED RICTOR WILD-TYPE 
          64.715           53.720 
[1] "15.8 - 202.7 (64.7)" "0.2 - 369.9 (53.7)" 
[1] "hr=" "1.2"
D116V3, continuous
                  vv
clus               I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  RICTOR MUTATED          0       0       2        1        2        1
  RICTOR WILD-TYPE       10       6      23        9       23       17
                  vv
clus               STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  RICTOR MUTATED           1         0         0         2          0
  RICTOR WILD-TYPE         9        14        10        34         14
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV
  RICTOR MUTATED            2          1        0
  RICTOR WILD-TYPE         24         42       16
D116V4, multiclass
            clus
vv           RICTOR MUTATED RICTOR WILD-TYPE
  I/II NOS                0               10
  STAGE 0                 0                6
  STAGE I                 2               23
  STAGE IA                1                9
  STAGE IB                2               23
  STAGE II                1               17
  STAGE IIA               1                9
  STAGE IIB               0               14
  STAGE IIC               0               10
  STAGE III               2               34
  STAGE IIIA              0               14
  STAGE IIIB              2               24
  STAGE IIIC              1               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
  RICTOR MUTATED       3  3  3  1
  RICTOR WILD-TYPE    50 59 57 54
D116V5, multiclass
       clus
vv      RICTOR MUTATED RICTOR WILD-TYPE
  T0+T1              3               50
  T2                 3               59
  T3                 3               57
  T4                 1               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RICTOR MUTATED     7   2   2   0
  RICTOR WILD-TYPE 136  51  32  35
D116V6, multiclass
    clus
vv   RICTOR MUTATED RICTOR WILD-TYPE
  N0              7              136
  N1              2               51
  N2              2               32
  N3              0               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"
D116V7, binary
                  cls
clus                 0   1
  RICTOR MUTATED    11   0
  RICTOR WILD-TYPE 245  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RICTOR MUTATED     11    0
  RICTOR WILD-TYPE  245   17
   clus
vv  RICTOR MUTATED RICTOR WILD-TYPE
  0             11              245
  1              0               17
[1] 2 2
[1] FALSE
D116V8, binary
                  cls
clus                 0   1
  RICTOR MUTATED     5   1
  RICTOR WILD-TYPE 102  72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RICTOR MUTATED      5    1
  RICTOR WILD-TYPE  102   72
     clus
vv    RICTOR MUTATED RICTOR WILD-TYPE
  NO               5              102
  YES              1               72
[1] 2 2
[1] FALSE
D116V9, binary
                  cls
clus                 0   1
  RICTOR MUTATED     2  10
  RICTOR WILD-TYPE  35 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RICTOR MUTATED      2   10
  RICTOR WILD-TYPE   35  243
     clus
vv    RICTOR MUTATED RICTOR WILD-TYPE
  NO               2               35
  YES             10              243
[1] 2 2
[1] FALSE
D116V10, continuous
D116V11, binary
                  cls
clus                 0   1
  RICTOR MUTATED     4   8
  RICTOR WILD-TYPE 105 173
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RICTOR MUTATED      4    8
  RICTOR WILD-TYPE  105  173
        clus
vv       RICTOR MUTATED RICTOR WILD-TYPE
  FEMALE              4              105
  MALE                8              173
[1] 2 2
[1] FALSE
D116V12, binary
                  cls
clus                 0   1
  RICTOR MUTATED     9   3
  RICTOR WILD-TYPE 245  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RICTOR MUTATED      9    3
  RICTOR WILD-TYPE  245   32
     clus
vv    RICTOR MUTATED RICTOR WILD-TYPE
  NO               9              245
  YES              3               32
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RICTOR MUTATED       0                         0    12
  RICTOR WILD-TYPE     5                         1   272
D116V13, multiclass
                           clus
vv                          RICTOR MUTATED RICTOR WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                 12              272
[1] 3 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
  RICTOR MUTATED     0  12
  RICTOR WILD-TYPE   3 271
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RICTOR MUTATED      0   12
  RICTOR WILD-TYPE    3  271
                        clus
vv                       RICTOR MUTATED RICTOR WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             12              271
[1] 2 2
[1] FALSE

Clustering(117) Variable = MED17 MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2               0   1
  MED17 MUTATED     2   1
  MED17 WILD-TYPE  95 102
  MED17 MUTATED MED17 WILD-TYPE 
              3             197 
  MED17 MUTATED MED17 WILD-TYPE 
              1             102 
$`MED17 MUTATED`
TCGA-EE-A20C TCGA-FS-A1ZM TCGA-FS-A1ZS 
       75.55        78.61       136.27 

$`MED17 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q1 
       52.90       134.40        27.35        19.04        36.85         8.42 
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       15.72        31.89       110.93        49.35       133.25        19.04 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       76.41        62.60        25.64        45.99        62.86        15.75 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      168.00        86.30       107.61        36.30       171.58        64.83 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       66.08        43.53        58.06       140.98        40.01        59.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34        90.21        23.67       173.85        30.67 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      144.46        31.76        62.70        11.34        42.05        45.70 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
      177.86        15.02        22.29        69.21        22.85        76.34 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
      138.67        68.68       150.61       110.53        60.10        64.83 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       58.85        30.44       225.11        42.64         3.91        16.41 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       52.41        18.21        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       26.24        79.20        75.22        76.14        12.99         0.26 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       44.28        47.41        47.74        27.16        61.12       346.49 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
      185.19       115.43        30.02        77.98        26.14        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        93.63 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        0.76         0.20        71.31        81.99       103.13        15.25 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
        5.75        23.77       209.79        94.19       171.85        63.25 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       89.26       104.78       145.45       227.01       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        6.28        67.89       111.85        45.90         3.35       168.85 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A 
       19.86       135.98        34.45        10.49         7.82         4.54 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       53.29        39.81        11.47       184.60       150.12        99.06 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       59.84        42.51       120.76        49.71        47.18       146.63 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       73.05        22.36         4.70        16.87        10.19        28.67 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN 
      173.29        68.52        15.48        32.05        74.47         4.50 
TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      174.21       171.78        49.74       195.98         8.35        27.62 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZQ 
      312.07        32.78        43.92         7.82        36.33       130.95 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       35.28         4.47        23.21         5.29         3.06        18.51 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       66.67       173.19        13.28        80.68        55.59        11.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90        18.25         1.91        53.29       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 
       96.92        17.06        42.48         7.59       120.53        34.49 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 
       46.92       297.01         7.23         0.20         0.33 

  MED17 MUTATED MED17 WILD-TYPE 
          75.55            0.00 
  MED17 MUTATED MED17 WILD-TYPE 
         136.27          346.49 
  MED17 MUTATED MED17 WILD-TYPE 
          78.61           46.92 
[1] "75.5 - 136.3 (78.6)" "0.0 - 346.5 (46.9)" 
[1] "hr=" "2.2"
D117V2, survival
                 sevent
clus2               0   1
  MED17 MUTATED     2   2
  MED17 WILD-TYPE 122 158
  MED17 MUTATED MED17 WILD-TYPE 
              4             280 
  MED17 MUTATED MED17 WILD-TYPE 
              2             158 
$`MED17 MUTATED`
TCGA-EE-A20C TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A266 
      151.27       101.26       148.80        10.13 

$`MED17 WILD-TYPE`
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       62.07        46.32        13.87        68.25        54.02        94.98 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR 
       68.15       168.26         2.60       340.14       126.81       134.40 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q1 
       27.35        31.40        50.76        15.45        36.95        16.57 
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-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        66.48        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-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-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       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         7.10        15.39 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29         9.90        25.18        77.56        22.95        76.57 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       144.89        20.38       222.51       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      135.02        88.87        53.92        65.92        40.60        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       33.93        10.49       225.96        43.36        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       20.35        29.29        58.92         7.04        36.46        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       27.22         8.65        33.73        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      133.81        91.56        13.55        63.35        85.08        78.97 
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-A29T TCGA-EE-A29V 
       56.42        66.74        14.47        61.28       369.93        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       115.96        59.64        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       86.14        59.28        67.43       173.79       220.24        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
      107.38        54.74        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       42.77        81.21        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       180.39       216.66 
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        64.04        28.77        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        41.59       138.81       172.18       127.20        36.95 
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       134.33 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      152.81        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       302.07       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        44.09       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       49.48         8.88       148.18       105.07        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        28.83        48.99        41.56       247.04        93.01 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A 
       46.98        33.21        12.95       149.03        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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       46.45         9.70        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41        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        34.03 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        54.41        80.68        17.46        55.59        13.51 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90        19.43         2.04        15.78       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        96.92        64.44        62.79        32.48        48.00 
TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      121.91        39.35        10.42        48.89        22.13       297.90 
TCGA-QB-A6FS TCGA-RP-A690 TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.20         0.33         0.69 

  MED17 MUTATED MED17 WILD-TYPE 
          10.13            0.20 
  MED17 MUTATED MED17 WILD-TYPE 
         151.27          369.93 
  MED17 MUTATED MED17 WILD-TYPE 
         125.03           53.72 
[1] "10.1 - 151.3 (125.0)" "0.2 - 369.9 (53.7)"  
[1] "hr=" "1.4"
D117V3, continuous
                 vv
clus              I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MED17 MUTATED          1       1       1        0        0        0         0
  MED17 WILD-TYPE        9       5      24       10       25       18        10
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MED17 MUTATED           0         0         1          0          0
  MED17 WILD-TYPE        14        10        35         14         26
                 vv
clus              STAGE IIIC STAGE IV
  MED17 MUTATED            0        0
  MED17 WILD-TYPE         43       16
D117V4, multiclass
            clus
vv           MED17 MUTATED MED17 WILD-TYPE
  I/II NOS               1               9
  STAGE 0                1               5
  STAGE I                1              24
  STAGE IA               0              10
  STAGE IB               0              25
  STAGE II               0              18
  STAGE IIA              0              10
  STAGE IIB              0              14
  STAGE IIC              0              10
  STAGE III              1              35
  STAGE IIIA             0              14
  STAGE IIIB             0              26
  STAGE IIIC             0              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
  MED17 MUTATED       0  3  0  0
  MED17 WILD-TYPE    53 59 60 55
D117V5, multiclass
       clus
vv      MED17 MUTATED MED17 WILD-TYPE
  T0+T1             0              53
  T2                3              59
  T3                0              60
  T4                0              55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MED17 MUTATED     3   0   1   0
  MED17 WILD-TYPE 140  53  33  35
D117V6, multiclass
    clus
vv   MED17 MUTATED MED17 WILD-TYPE
  N0             3             140
  N1             0              53
  N2             1              33
  N3             0              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"
D117V7, binary
                 cls
clus                0   1
  MED17 MUTATED     4   0
  MED17 WILD-TYPE 252  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED17 MUTATED      4    0
  MED17 WILD-TYPE  252   17
   clus
vv  MED17 MUTATED MED17 WILD-TYPE
  0             4             252
  1             0              17
[1] 2 2
[1] FALSE
D117V8, binary
                 cls
clus                0   1
  MED17 MUTATED     0   0
  MED17 WILD-TYPE 107  73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED17 MUTATED      0    0
  MED17 WILD-TYPE  107   73
D117V9, binary
                 cls
clus                0   1
  MED17 MUTATED     1   4
  MED17 WILD-TYPE  36 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED17 MUTATED      1    4
  MED17 WILD-TYPE   36  249
     clus
vv    MED17 MUTATED MED17 WILD-TYPE
  NO              1              36
  YES             4             249
[1] 2 2
[1] FALSE
D117V10, continuous
[1] "Remove cluster labels:" "MED17 MUTATED"         
clus
  MED17 MUTATED MED17 WILD-TYPE 
              2             210 
     TCGA-D3-A2JF      TCGA-D3-A3ML      TCGA-D3-A51G      TCGA-EB-A5SH 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A180      TCGA-EE-A184      TCGA-EE-A20H      TCGA-EE-A29L 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2GD      TCGA-EE-A2GO      TCGA-EE-A2MR      TCGA-ER-A198 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A1ZF      TCGA-D3-A1Q1      TCGA-D3-A1Q3      TCGA-D3-A1Q4 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A1Q6      TCGA-D3-A1Q7      TCGA-D3-A1Q9      TCGA-D3-A1QA 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A2J6      TCGA-D3-A2J7      TCGA-D3-A2J8      TCGA-D3-A2J9 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A2JA      TCGA-D3-A2JD      TCGA-D3-A2JG      TCGA-D3-A2JH 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A2JK      TCGA-D3-A3BZ      TCGA-D3-A3C6      TCGA-D3-A3CB 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-D3-A3MU      TCGA-D3-A3MV 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A51E      TCGA-D3-A51F      TCGA-D3-A51H      TCGA-D3-A51K 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A51R      TCGA-D3-A51T      TCGA-D3-A5GL      TCGA-D3-A5GN 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D3-A5GO      TCGA-D3-A5GR      TCGA-D3-A5GS      TCGA-D3-A5GU 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D9-A3Z1      TCGA-D9-A3Z3      TCGA-D9-A6E9      TCGA-D9-A6EA 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-D9-A6EC      TCGA-D9-A6EG      TCGA-DA-A1HW      TCGA-DA-A1HY 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-DA-A1I0      TCGA-DA-A1I4      TCGA-DA-A1I5      TCGA-DA-A1I8 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-DA-A1IA      TCGA-DA-A1IB      TCGA-DA-A1IC      TCGA-DA-A3F2 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-DA-A3F5      TCGA-DA-A3F8      TCGA-EB-A5UL      TCGA-EB-A5UN 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EB-A5VV      TCGA-EE-A17X      TCGA-EE-A17Y      TCGA-EE-A17Z 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A185      TCGA-EE-A20B 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A20F      TCGA-EE-A29A      TCGA-EE-A29B      TCGA-EE-A29C 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A29D      TCGA-EE-A29E      TCGA-EE-A29G      TCGA-EE-A29H 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A29M      TCGA-EE-A29P      TCGA-EE-A29Q      TCGA-EE-A29R 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29W      TCGA-EE-A29X 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2A0      TCGA-EE-A2A1      TCGA-EE-A2A2      TCGA-EE-A2A5 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2A6      TCGA-EE-A2GB      TCGA-EE-A2GC      TCGA-EE-A2GE 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2GH      TCGA-EE-A2GI      TCGA-EE-A2GJ      TCGA-EE-A2GK 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2GL      TCGA-EE-A2GM      TCGA-EE-A2GN      TCGA-EE-A2GP 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2GR      TCGA-EE-A2GS      TCGA-EE-A2GT      TCGA-EE-A2GU 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2M5      TCGA-EE-A2M6      TCGA-EE-A2M7      TCGA-EE-A2M8 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2MC      TCGA-EE-A2MD      TCGA-EE-A2ME      TCGA-EE-A2MF 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2MG      TCGA-EE-A2MH      TCGA-EE-A2MI      TCGA-EE-A2MJ 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2MK      TCGA-EE-A2ML      TCGA-EE-A2MM      TCGA-EE-A2MN 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2MP      TCGA-EE-A2MQ      TCGA-EE-A2MS      TCGA-EE-A2MT 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A2MU      TCGA-EE-A3AE      TCGA-EE-A3AH      TCGA-EE-A3J3 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A3J4      TCGA-EE-A3J5      TCGA-EE-A3J7      TCGA-EE-A3J8 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A3JA      TCGA-EE-A3JB      TCGA-EE-A3JE      TCGA-EE-A3JH 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-EE-A3JI      TCGA-ER-A197      TCGA-ER-A199      TCGA-ER-A19C 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19E      TCGA-ER-A19F      TCGA-ER-A19G 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-ER-A19H      TCGA-ER-A19M      TCGA-ER-A19Q      TCGA-ER-A19T 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-ER-A19W      TCGA-ER-A2NC      TCGA-ER-A2ND      TCGA-ER-A2NF 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-ER-A2NG      TCGA-ER-A2NH      TCGA-ER-A3ET      TCGA-ER-A3EV 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-ER-A3PL      TCGA-ER-A42K      TCGA-ER-A42L      TCGA-FR-A3YN 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FR-A44A      TCGA-FS-A1YW      TCGA-FS-A1YX      TCGA-FS-A1YY 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A1Z0      TCGA-FS-A1Z4      TCGA-FS-A1Z7      TCGA-FS-A1ZA 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A1ZB      TCGA-FS-A1ZD      TCGA-FS-A1ZE      TCGA-FS-A1ZG 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A1ZH      TCGA-FS-A1ZJ      TCGA-FS-A1ZK      TCGA-FS-A1ZP 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A1ZR      TCGA-FS-A1ZT      TCGA-FS-A1ZU      TCGA-FS-A1ZW 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A1ZY      TCGA-FS-A1ZZ      TCGA-FS-A4F0      TCGA-FS-A4F4 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A4F5      TCGA-FS-A4F8      TCGA-FS-A4F9      TCGA-FS-A4FB 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-FS-A4FC      TCGA-FS-A4FD      TCGA-FW-A3TV      TCGA-GF-A6C8 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-GN-A262      TCGA-GN-A264      TCGA-GN-A267      TCGA-GN-A268 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D      TCGA-GN-A4U3      TCGA-GN-A4U4 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" "MED17 WILD-TYPE" 
     TCGA-GN-A4U7      TCGA-GN-A4U9 
"MED17 WILD-TYPE" "MED17 WILD-TYPE" 
D117V11, binary
                 cls
clus                0   1
  MED17 MUTATED     1   4
  MED17 WILD-TYPE 108 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED17 MUTATED      1    4
  MED17 WILD-TYPE  108  177
        clus
vv       MED17 MUTATED MED17 WILD-TYPE
  FEMALE             1             108
  MALE               4             177
[1] 2 2
[1] FALSE
D117V12, binary
                 cls
clus                0   1
  MED17 MUTATED     4   1
  MED17 WILD-TYPE 250  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED17 MUTATED      4    1
  MED17 WILD-TYPE  250   34
     clus
vv    MED17 MUTATED MED17 WILD-TYPE
  NO              4             250
  YES             1              34
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED17 MUTATED       0                         0     5
  MED17 WILD-TYPE     5                         1   279
D117V13, multiclass
                           clus
vv                          MED17 MUTATED MED17 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 5             279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V14, binary
                 cls
clus                0   1
  MED17 MUTATED     0   5
  MED17 WILD-TYPE   3 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED17 MUTATED      0    5
  MED17 WILD-TYPE    3  278
                        clus
vv                       MED17 MUTATED MED17 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5             278
[1] 2 2
[1] FALSE
